Document and Entity Information - shares	3 Months Ended
Document and Entity Information - shares	Mar. 31, 2017	Apr. 28, 2017
Document and Entity Information
Entity Registrant Name	T2 Biosystems, Inc.
Entity Central Index Key	0001492674
Document Type	10-Q
Document Period End Date	Mar. 31, 2017
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		30,594,342
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	Q1

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 58,822	$ 73,488
Accounts receivable	409	327
Prepaid expenses and other current assets	931	820
Inventories, net	489	803
Total current assets	60,651	75,438
Property and equipment, net	14,468	13,589
Restricted cash	260	260
Other assets	280	281
Total assets	75,659	89,568
Current liabilities:
Accounts payable	1,161	962
Accrued expenses and other current liabilities	4,060	4,908
Current portion of notes payable	1,316	1,269
Deferred revenue	2,127	2,445
Current portion of lease incentives	249	301
Total current liabilities	8,913	9,885
Notes payable, net of current portion	39,750	39,504
Lease incentives, net of current portion	791	792
Other liabilities	175	49
Commitments and contingencies
Stockholders’ equity:
Preferred stock, $0.001 par value; 10,000,000 shares authorized; no shares issued and outstanding at March 31, 2017 and December 31, 2016	0	0
Common stock, $0.001 par value; 200,000,000 shares authorized; 30,594,342 and 30,482,712 shares issued and outstanding at March 31, 2017 and December 31, 2016, respectively	31	30
Additional paid-in capital	244,391	242,997
Accumulated deficit	(218,392)	(203,689)
Total stockholders’ equity	26,030	39,338
Total liabilities and stockholders’ equity	$ 75,659	$ 89,568

Condensed Consolidated Balance Sheet (Parentheticals) - $ / shares	Mar. 31, 2017	Dec. 31, 2016
Statement of Financial Position [Abstract]
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized	10,000,000	10,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	30,594,342	30,482,712
Common stock, shares outstanding	30,594,342	30,482,712

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Revenues [Abstract]
Product revenue	$ 631	$ 437
Research revenue	310	659
Total revenue	941	1,096
Costs and expenses:
Cost of product revenue	1,627	1,026
Research and development	6,585	6,589
Selling, general and administrative	5,874	6,204
Total costs and expenses	14,086	13,819
Loss from operations	(13,145)	(12,723)
Interest expense, net	(1,637)	(735)
Other income, net	79	32
Net loss and comprehensive loss	$ (14,703)	$ (13,426)
Net loss per share — basic and diluted (USD per share)	$ (0.48)	$ (0.55)
Weighted-average number of common shares used in computing net loss per share — basic and diluted (in shares)	30,531,180	24,218,767

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Operating activities
Net loss	$ (14,703)	$ (13,426)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	694	529
Stock-based compensation expense	1,157	1,290
Non-cash interest expense	639	148
Deferred rent	(53)	(60)
Changes in operating assets and liabilities:
Accounts receivable	(82)	9
Prepaid expenses and other assets	(111)	(56)
Inventories, net	314	(576)
Accounts payable	199	679
Accrued expenses and other liabilities	(494)	36
Deferred revenue	(318)	(409)
Net cash used in operating activities	(12,758)	(11,836)
Investing activities
Purchases and manufacture of property and equipment	(1,594)	(2,158)
Net cash used in investing activities	(1,594)	(2,158)
Financing activities
Payment of offering costs for issuance of common stock in public offering	0	(370)
Proceeds from issuance of common stock and stock options exercises, net	339	301
Payments of issuance costs for notes payable	(354)	0
Repayments of note payable	(299)	(80)
Net cash used in financing activities	(314)	(149)
Net decrease in cash and cash equivalents	(14,666)	(14,143)
Cash and cash equivalents at beginning of period	73,488	73,662
Cash and cash equivalents at end of period	58,822	59,519
Supplemental disclosures of cash flow information
Cash paid for interest	993	517
Supplemental disclosures of noncash investing and financing activities
Accrued property and equipment	$ 61	$ 132

Nature of Business	3 Months Ended
Nature of Business	Mar. 31, 2017
Nature of Business
Nature of Business	Nature of Business T2 Biosystems, Inc. (the “Company”) was incorporated on April 27, 2006 as a Delaware corporation with operations based in Lexington, Massachusetts. The Company is an in vitro diagnostics company that has developed an innovative and proprietary technology platform that offers a rapid, sensitive and simple alternative to existing diagnostic methodologies. The Company is using its T2 Magnetic Resonance technology ("T2MR") to develop a broad set of applications aimed at lowering mortality rates, improving patient outcomes and reducing the cost of healthcare by helping medical professionals make targeted treatment decisions earlier. T2MR enables rapid detection of pathogens, biomarkers and other abnormalities in a variety of unpurified patient sample types, including whole blood, plasma, serum, saliva, sputum and urine, and can detect cellular targets at limits of detection as low as one colony forming unit per milliliter ("CFU/mL"). The Company’s initial development efforts target sepsis and Lyme disease, which are areas of significant unmet medical need in which existing therapies could be more effective with improved diagnostics. On September 22, 2014, the Company received market clearance from the U.S. Food and Drug Administration (“FDA”) for its first two products, the T2Dx Instrument (the “T2Dx”) and T2Candida Panel (“T2Candida”). Liquidity At March 31, 2017, the Company has cash and cash equivalents of $58.8 million and an accumulated deficit of $218.4 million. The future success of the Company is dependent on its ability to successfully commercialize its FDA approved products, obtain regulatory clearance for and successfully launch its future product candidates, obtain additional capital and ultimately attain profitable operations. Historically, the Company has funded its operations primarily through its August 2014 initial public offering, its December 2015 secondary public offering, its September 2016 private investment in public equity (“PIPE”) financing, private placements of redeemable convertible preferred stock and through debt financing arrangements. The Company is subject to a number of risks similar to other newly commercial life science companies, including, but not limited to commercially launching the Company’s products, development and market acceptance of the Company’s product candidates, development by its competitors of new technological innovations, protection of proprietary technology, and raising additional capital. Having obtained authorization from the FDA to market T2Dx and T2Candida, the Company has incurred significant commercialization expenses related to product sales, marketing, manufacturing and distribution. In addition, the Company expects that costs and expenses may increase as it continues the research and development of other product candidates and maintains, expands and protects its intellectual property portfolio. The Company may seek to fund its operations through public equity or private equity or debt financings, as well as other sources. However, the Company may be unable to raise additional funds or enter into such other arrangements when needed on favorable terms or at all. The Company’s failure to raise capital or enter into such other arrangements if and when needed would have a negative impact on the Company’s business, results of operations and financial condition and the Company’s ability to develop and commercialize T2Dx, T2Candida and other product candidates. Management believes that its existing cash and cash equivalents at March 31, 2017, together with the additional remaining liquidity of up to $1.5 million available under an Equipment Lease Credit Facility (the “Credit Facility”) entered into in October 2015 to help the Company meet its capital equipment needs (Note 5), will be sufficient to allow the Company to fund its current operating plan for at least the next 12 months. Should the Company’s current operating plans not materialize as expected, and it is unable to obtain additional capital on a timely basis, the Company may be required to change its current operating plans to reduce its future expenses, which is within its control, in order to fund operations at reduced levels. For more information, refer to the section titled “Liquidity and Capital Resources” in Item 2, Management’s Discussion and Analysis of Financial Condition and Results of Operations and the section entitled “Risk Factors” in the Annual Report on Form 10-K for the year ended December 31, 2016, for additional risks associated with our capital needs.

Summary of Significant Accounting Policies	3 Months Ended
Summary of Significant Accounting Policies	Mar. 31, 2017
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	Summary of Significant Accounting Policies Basis of Presentation The Company’s financial statements have been prepared in conformity with generally accepted accounting principles in the United States of America (“GAAP”). Any reference in these notes to applicable guidance is meant to refer to the authoritative United States GAAP as defined in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASU”) of the Financial Accounting Standards Board (“FASB”). The Company’s condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiary, T2 Biosystems Securities Corporation. All intercompany balances and transactions have been eliminated. We have evaluated subsequent events from March 31, 2017 through the date of the issuance of these consolidated financial statements and have determined that no material subsequent events have occurred that would affect the information presented in these consolidated financial statements. Unaudited Interim Financial Information Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016. The accompanying interim condensed consolidated balance sheet as of March 31, 2017, the condensed consolidated statements of operations and comprehensive loss for the three months ended March 31, 2017 and 2016, the condensed consolidated statements of cash flows for the three months ended March 31, 2017 and 2016 and the related financial data and other information disclosed in these notes are unaudited. The unaudited interim financial statements have been prepared on the same basis as the audited annual financial statements, and, in the opinion of management, reflect all adjustments, consisting of normal recurring adjustments, necessary for the fair presentation of the Company’s financial position as of March 31, 2017, and the results of its operations and its cash flows for the three months ended March 31, 2017 and 2016. The results for the three months ended March 31, 2017 are not necessarily indicative of the results to be expected for the year ending December 31, 2017, any other interim periods, or any future year or period. Segment Information Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision maker, or decision‑making group, in deciding how to allocate resources and in assessing performance. The Company’s chief operating decision maker is the Chief Executive Officer. The Company views its operations and manages its business in one operating segment, which is the business of developing and, upon regulatory clearance, launching commercially its diagnostic products aimed at lowering mortality rates, improving patient outcomes and reducing the cost of healthcare by helping medical professionals make targeted treatment decisions earlier. Net Loss Per Share Basic net loss per share is calculated by dividing net loss by the weighted-average number of shares of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is calculated by adjusting the weighted-average number of shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury-stock method. For purposes of the diluted net loss per share calculation, stock options and unvested restricted stock are considered to be common stock equivalents, but have been excluded from the calculation of diluted net loss per share, as their effect would be anti-dilutive for all periods presented. Therefore, basic and diluted net loss per share applicable to common stockholders was the same for all periods presented. Guarantees As permitted under Delaware law, the Company indemnifies its officers and directors for certain events or occurrences while each such officer or director is, or was, serving at the Company’s request in such capacity. The term of the indemnification is the officer’s or director’s lifetime. The maximum potential amount of future payments the Company could be required to make is unlimited; however, the Company has directors’ and officers’ liability insurance coverage that limits its exposure and enables the Company to recover a portion of any future amounts paid. The Company leases office, laboratory and manufacturing space under noncancelable operating leases. The Company has standard indemnification arrangements under the leases that require it to indemnify the landlords against all costs, expenses, fines, suits, claims, demands, liabilities, and actions directly resulting from any breach, violation or nonperformance of any covenant or condition of the Company’s leases. In the ordinary course of business, the Company enters into indemnification agreements with certain suppliers and business partners where the Company has certain indemnification obligations limited to the costs, expenses, fines, suits, claims, demands, liabilities and actions directly resulting from the Company’s gross negligence or willful misconduct, and in certain instances, breaches, violations or nonperformance of covenants or conditions under the agreements. As of March 31, 2017 and December 31, 2016, the Company had not experienced any material losses related to these indemnification obligations, and no material claims with respect thereto were outstanding. The Company does not expect significant claims related to these indemnification obligations and, consequently, concluded that the fair value of these obligations is negligible, and no related reserves were established. Revenue Recognition The Company generates revenue from product sales, which includes the sale of instruments, consumable diagnostic tests and related services, and research and development agreements with third parties. The Company recognizes revenue in accordance with FASB ASC Topic 605, Revenue Recognition (“ASC 605”). Accordingly, the Company recognizes revenue when all of the following criteria have been met: i. Persuasive evidence of an arrangement exists ii. Delivery has occurred or services have been rendered iii. The seller’s price to the buyer is fixed or determinable iv. Collectability is reasonably assured If any of the above criteria have not been met, the Company defers revenue until such time each of the criteria have been satisfied. Product revenue is generated by the sale of instruments and consumable diagnostic tests predominantly through the Company's direct sales force in the United States and distributors in geographic regions outside the United States. The Company does not offer product return or exchange rights (other than those relating to defective goods under warranty) or price protection allowances to its customers, including its distributors. Payment terms granted to distributors are the same as those granted to end-user customers and payments are not dependent upon the distributors’ receipt of payment from their end-user customers. The Company either sells instruments to customers and international distributors, or retains title and places the instrument at the customer site pursuant to a reagent rental agreement. When the instrument is directly purchased by a customer, the Company recognizes revenue when all applicable revenue recognition criteria are met. When the instrument is placed under a reagent rental agreement, the Company’s customers generally agree to fixed term agreements, which can be extended, certain of which may include minimum purchase commitments and/or incremental charges on each consumable diagnostic test purchased, which varies based on the volume of test cartridges purchased. Revenue from the sale of consumable diagnostic tests, which includes the incremental charge, is recognized upon delivery as a component of product revenue in the Company’s consolidated statements of operations and comprehensive loss. Direct sales of instruments include warranty, maintenance and technical support services for one year following the installation of the purchased instrument (“Maintenance Services”). After the completion of the initial Maintenance Services period, customers have the option to renew the Maintenance Services for additional one year periods in exchange for additional consideration. In addition, the Company may provide training to customers. The Company defers revenue from the initial sale of the instrument equal to the relative fair value of the one year of Maintenance Services and training and recognizes the amounts ratably over the service delivery period. The Company warrants that consumable diagnostic tests will be free from defects, when handled according to product specifications, for the stated life of the product. To fulfill valid warranty claims, the Company either provides a credit to its customers on future orders or provides a replacement product. Accordingly, the Company defers revenue associated with the estimated defect rates of the consumable diagnostic tests. The Company does not offer rights of return for instruments or consumable diagnostic tests. Shipping and handling costs incurred associated with products sold to customers are recorded as a cost of product revenue in the consolidated statement of operations and comprehensive loss. Shipping and handling costs billed to customers in connection with a product sale are recorded as a component of product revenue in the consolidated statements of operations and comprehensive loss. For multiple-element arrangements, the Company identifies the deliverables included within each agreement and evaluates which deliverables represent separate units of accounting. The determination that multiple elements in an arrangement meet the criteria for separate units of accounting requires the Company’s management to exercise judgment. The Company accounts for those components as separate elements when the following criteria are met: (1) the delivered items have value to the customer on a stand-alone basis; and, (2) if there is a general right of return relative to the delivered items, delivery or performance of the undelivered items is considered probable and within its control. The consideration received is allocated among the separate units of accounting based on a selling price hierarchy. The selling price hierarchy is based on: (1) vendor specific objective evidence (“VSOE”), if available; (2) third party evidence of selling price if VSOE is not available; or (3) best estimated selling price (“BESP”) if neither VSOE nor third party evidence is available. The Company generally expects that it will not be able to establish selling price using third-party evidence due to the nature of our products and the markets in which the Company competes, and, as such, the Company typically will determine selling price using VSOE or BESP. When the Company establishes selling price using BESP, consideration is given to both market and Company-specific factors, including the cost to produce the deliverable and the anticipated margin on that deliverable, as well as the characteristics of markets in which the deliverable is sold. Revenue earned from activities performed pursuant to research and development agreements is reported as research revenue in the consolidated statements of operations and comprehensive loss, using the proportional performance method as the work is completed, limited to payments earned, and the related costs are expensed as incurred as research and development expense. The timing of receipt of cash from the Company’s research and development agreements generally differs from when revenue is recognized. Product Recall In July 2016, the Company initiated a voluntary recall and replacement of its T2Candida cartridges at certain customer sites because T2Candida was experiencing higher than normal invalid test rates as the T2Candida cartridges aged. As of June 30, 2016, as a result of this voluntary recall, the Company deferred revenue totaling $0.1 million and recorded additional costs of product revenue of $41,000 related to returned products, which are no longer usable. As of March 31, 2017, the Company had $37,000 of deferred revenue and $2,000 of warranty reserve remaining, both related to this voluntary recall. The impact of the voluntary recall on T2Candida cartridges in inventory was not material to the condensed consolidated financial statements. Cost of Product Revenue Cost of product revenue includes the cost of materials, direct labor and manufacturing overhead costs used in the manufacture of consumable diagnostic tests sold to customers and related license and royalty fees. Cost of product revenue also includes depreciation on revenue generating T2Dx that have been placed with customers under reagent rental agreements; costs of materials, direct labor and manufacturing overhead costs on the T2Dx sold to customers; and other costs such as customer support costs, royalties and license fees, warranty and repair and maintenance expense on the T2Dx that have been placed with customers under reagent rental agreements. Research and Development Costs Costs incurred in the research and development of the Company’s product candidates are expensed as incurred. Research and development expenses consist of costs incurred in performing research and development activities, including activities associated with performing services under research revenue arrangements, and include salaries and benefits, stock compensation, research‑related facility and overhead costs, laboratory supplies, equipment and contract services. Recent Accounting Standards From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption. Accounting Standards Adopted In July 2015, the FASB issued ASU No. 2015-11, Inventory (Topic 330): Simplifying the Measurement of Inventory (“ASU 2015-11”). The standard simplifies the subsequent measurement of inventory by requiring inventory to be measured at the lower of cost and net realizable value for entities using the first-in-first out method of valuing inventory. ASU 2015-11 eliminates other measures required by current guidance to determine net realizable value. ASU 2015-11 is effective for fiscal years beginning after December 15, 2016 and interim periods within those fiscal years and early adoption is permitted. The Company's adoption of this standard did not have a material effect on its condensed consolidated financial statements. In March 2016, the FASB released ASU No. 2016-09 Improvements to Employee Share-Based Payment Accounting (“ASU 2016-09”) which is intended to simplify income tax accounting for excess tax benefits, accounting for forfeitures, and employer statutory withholding. Under the current guidance, excess tax benefits that result from an award vesting or settling are recognized in additional paid-in capital in the period that they reduce cash taxes payable. This requires the provision to be computed on a with and without option basis and may result in net operating loss and credit carryforwards on the balance sheet being less than what is available on the tax return. Under the new guidance, the income tax effects of awards will be recognized as a component of income tax expense when the awards vest or are settled (regardless if cash taxes are reduced). For interim reporting purposes, companies will account for excess tax benefits and tax deficiencies as discrete items in the period during which they occurred. The guidance is effective for public entities for fiscal years beginning after December 15, 2016, and interim periods within those years. Early adoption is permitted, however all of the guidance included in the update must be applied when adopted. The Company must use a modified retrospective transition method for adopting and record the cumulative effect of all unrecognized benefits and any change in valuation allowances at the end of the prior tax period as an adjustment to retained earnings. The Company's adoption of this standard did not have a material effect on its condensed consolidated financial statements and prior periods have not been adjusted. As a result, the Company established a net operating loss deferred tax asset of $1.2 million to account for prior period excess tax benefits through retained earnings, however an offsetting valuation allowance of $1.2 million will also be established through retained earnings because it is not more likely than not that the deferred tax asset will be realized due to historical and expected future losses, such that there is no impact on the Company’s condensed consolidated financial statements. The Company also elected to maintain the use of estimated forfeitures in the calculation of stock based compensation. In March 2016, the FASB issued ASU No. 2016-06, Derivatives and Hedging (Topic 815): Contingent Put and Call Options in Debt Instruments (“ASU 2016-06”), which applies to all issuers of or investors in debt instruments with embedded call or put options. ASU 2016-06 clarifies the requirements for assessing whether contingent call or put options that can accelerate the payment of principal on debt instruments are clearly and closely related to their debt hosts. Entities performing the assessment under the guidance of ASU 2016-06 are required to assess the embedded call or put options solely in accordance with the four-step decision process. In addition, ASU 2016-06 clarifies what steps are required when assessing whether the economic characteristics and risks of call or put options are clearly and closely related to the economic characteristics and risks of their debt hosts. ASU 2016-06 is effective for financial statements issued for fiscal years beginning after December 15, 2016 and interim periods within those fiscal years using the modified retrospective method for existing debt instruments. The Company's adoption of this standard did not have a material effect on its condensed consolidated financial statements. Accounting Standards Issued, Not Adopted In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments ("ASC 2016-15"), which provides guidance on the classification of certain specific cash flow issues including debt prepayment or extinguishment costs, settlement of certain debt instruments, contingent consideration payments made after a business combination, proceeds from the settlement of certain insurance claims and distributions received from equity method investees. The standard requires the use of a retrospective approach to all periods presented, but may be applied prospectively if retrospective application would be impracticable. The guidance is effective for public entities for fiscal years beginning after December 15, 2017, and interim periods within those years, and early application is permitted. The Company is currently evaluating the impact of its pending adoption of ASU 2016-15 on the Company’s consolidated financial statements. In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which applies to all leases. Under ASU 2016-02, a right-of-use asset and lease obligation will be recorded for all leases, whether operating or financing leases, while the statement of operations will reflect lease expense for operating leases and amortization and interest expense for financing leases. ASU 2016-02 is effective for fiscal years beginning after December 15, 2018 and interim periods within those years, which is the year ended December 31, 2019 for the Company. Entities are required to use a modified retrospective approach of adoption for leases that exist or are entered into after the beginning of the earliest comparative period in the financial statements. Full retrospective application is prohibited. The Company is evaluating the new guidance and the expected effect on the Company’s consolidated financial statements. In June 2014, the FASB issued amended guidance, ASU No. 2014-09, Revenue from Contracts with Customers (“ASU 2014-09”), which is applicable to revenue recognition that will now be effective for the Company for the year ending December 31, 2018, as a result of the deferral of the effective date adopted by the FASB in July 2015. The new guidance must be adopted using either a full retrospective approach for all periods presented or a modified retrospective approach. Early adoption prior to the original adoption date of ASU 2014-09 is not permitted. The new guidance applies a more principles-based approach to revenue recognition. The Company currently anticipates adoption of the new standard effective January 1, 2018 under the full retrospective method. The Company’s revenue is primarily comprised of product sales and research services, and the Company is in the process of determining the impact of the new standard on its financial statements.

Fair Value Measurements

3 Months Ended

Mar. 31, 2017

Fair Value Disclosures [Abstract]

Fair Value Measurements

The Company measures the following financial assets at fair value on a recurring basis. There were no transfers between levels of the fair value hierarchy during any of the periods presented. The following tables set forth the Company’s financial assets carried at fair value categorized using the lowest level of input applicable to each financial instrument as of March 31, 2017 and December 31, 2016 (in thousands):



	Balance at December 31, 2017		Quoted Prices in Active Markets for Identical Assets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Assets:
Cash	$	6,702	$	6,702	$	—	$	—
Money market funds	52,120		52,120		—		—
Restricted cash	260		260		—		—
Total	$	59,082	$	59,082	$	—	$	—



	Balance at December 31, 2016		Quoted Prices in Active Markets for Identical Assets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Assets:
Cash	$	16,887	$	16,887	$	—	$	—
Money market funds	56,601		56,601		—		—
Restricted cash	260		260		—		—
Total	$	73,748	$	73,748	$	—	$	—

For certain financial instruments, including accounts payable and accrued expenses, the carrying amounts approximate their fair values as of March 31, 2017 and December 31, 2016 because of their short-term nature. At March 31, 2017 and December 31, 2016, the carrying value of the Company’s debt approximated fair value, which was determined using Level 3 inputs, using market quotes from brokers and is based on current rates offered for similar debt (Note 5).

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Supplemental Balance Sheet Information

3 Months Ended

Mar. 31, 2017

Balance Sheet Related Disclosures [Abstract]

Supplemental Balance Sheet Information

Inventories

Inventories are stated at the lower of cost or net realizable value on a first-in, first-out basis and are comprised of the following (in thousands):



	March 31, 2017		December 31, 2016
Raw materials	$	215	$	389
Work-in-process	262		351
Finished goods	12		63
Total inventories, net	$	489	$	803

Property and Equipment

Property and equipment consists of the following (in thousands):



	March 31, 2017			December 31, 2016
Office and computer equipment	$	409		$	409
Software	743			708
Laboratory equipment	4,562			4,516
Furniture	200			200
Manufacturing equipment	910			897
Manufacturing tooling and molds	154			154
T2-owned instruments and components	10,522			9,119
Leasehold improvements	3,353			3,353
Construction in progress	1,343			1,299
	22,196			20,655
Less accumulated depreciation and amortization	(7,728		)	(7,066		)
Property and equipment, net	$	14,468		$	13,589

Construction in progress is primarily comprised of equipment and leasehold improvement construction projects that have not been placed in service. T2-owned instruments and components is comprised of raw materials and work-in-process inventory that are expected to be used or used to produce Company-owned instruments, based on our business model and forecast, and completed instruments that will be used for internal research and development, clinical studies or reagent rental agreements with customers. Completed T2-owned instruments are placed in service once installation procedures are completed and are depreciated over five years. The Company has approximately $6.7 million and $5.7 million of net value related to the T2-owned instruments installed and depreciating as of March 31, 2017 and December 31, 2016, respectively. Depreciation expense for T2-owned instruments placed at customer sites pursuant to reagent rental agreements is recorded as a component of cost of product revenue and totaled approximately $0.2 million and $0.1 million for the three months ended March 31, 2017 and March 31, 2016, respectively. Depreciation expense for T2-owned instruments used for internal research and development and clinical studies is recorded as a component of research and development expense.

Accrued Expenses

Accrued expenses consist of the following (in thousands):



	March 31, 2017		December 31, 2016
Accrued payroll and compensation	$	1,848	$	2,479
Accrued research and development expenses	724		846
Accrued professional services	915		884
Other accrued expenses	573		699
Total accrued expenses	$	4,060	$	4,908

Notes Payable

3 Months Ended

Mar. 31, 2017

Debt Disclosure [Abstract]

Notes Payable

Future principal payments on the notes payable are as follows (in thousands):



	March 31, 2017			December 31, 2016
Term loan agreement, net of deferred issuance costs of $2.9 million and $3.0 million, respectively	$	37,624		$	37,031
Equipment lease credit facility, net of deferred issuance cost of $40,000 and $45,000, respectively	3,442			3,742
Total notes payable	41,066			40,773
Less: current portion of notes payable	(1,316		)	(1,269		)
Notes payable, net of current portion	$	39,750		$	39,504

Term Loan Agreement

In December 2016, the Company entered into a Term Loan Agreement (the “Term Loan Agreement”) with CRG Servicing LLC (“CRG”). The Company initially borrowed $40.0 million pursuant to the Term Loan Agreement and may borrow up to an additional $10.0 million at any time through and including July 27, 2018, provided that, among other conditions, the Company receives 510(k) clearance for the marketing of T2Bacteria^TM by the U.S. Food and Drug Administration (“FDA”) on or before April 30, 2018 (the “Approval Milestone”). The Term Loan Agreement has a six-year term with three years (through December 30, 2019) of interest-only payments, which period shall be extended to four years (through December 30, 2020) if the Company achieves the Approval Milestone, after which quarterly principal and interest payments will be due through the December 30, 2022 maturity date. Interest on the amounts borrowed under the Term Loan Agreement accrues at an annual fixed rate of (a) prior to the Approval Milestone, 12.5%, 4.0% of which may be deferred during the interest-only period by adding such amount to the aggregate principal loan amount and (b) following the Approval Milestone, 11.5%, 3.5% of which may be deferred during the interest-only period by adding such amount to the aggregate principal loan amount. In addition, if the Company achieves certain financial performance metrics, the loan will convert to interest-only until the December 30, 2022 maturity, at which time all unpaid principal and accrued unpaid interest will be due and payable. The Company is required to pay CRG a financing fee based on the loan principal amount drawn. The Company is also required to pay a final payment fee of 8% of the principal outstanding upon repayment.

The Company may prepay all or a portion of the outstanding principal and accrued unpaid interest under the Term Loan Agreement at any time upon prior notice subject to a prepayment fee during the first five years of the term and no prepayment fee thereafter. As security for its obligations under the Term Loan Agreement the Company entered into a security agreement with CRG whereby the Company granted a lien on substantially all of its assets, including intellectual property. The Term Loan Agreement also contains customary affirmative and negative covenants for a credit facility of this size and type. The Term Loan Agreement also requires the Company to achieve certain revenue targets, whereby the Company is required to pay double the amount of any shortfall as an acceleration of principal payments. The Term Loan Agreement includes a subjective acceleration clause whereby an event of default, including a material adverse change in the business, operations, or conditions (financial or otherwise), could result in the acceleration of the obligations under the Term Loan Agreement. Under certain circumstances, a default interest rate of an additional 4.0% per annum will apply at the election of CRG on all outstanding obligations during the occurrence and continuance of an event of default. CRG has not exercised its right under this clause, as there have been no such events. The Company believes the likelihood of CRG exercising this right is remote.

The Company assessed the terms and features of the Term Loan Agreement in order to identify any potential embedded features that would require bifurcation or any beneficial conversion features. As part of this analysis, the Company assessed the economic characteristics and risks of the Term Loan Agreement, including put and call features. The Company determined that the features of the Term Loan Agreement are either clearly and closely associated with a debt host and do not require bifurcation as a derivative liability, or the fair value of the feature is immaterial. Included in these features are principal payment acceleration clauses triggered by a developmental milestone. Should the Company’s assessment of this milestone change, there could be a non-cash charge in operations. The Company will continue to reassess the features to determine if they require separate accounting on a quarterly basis.

In December 2016, pursuant to the Term Loan Agreement, the Company made an initial draw of $39.2 million, net of financing fees. The Company used approximately $28.0 million of the initial proceeds to repay approximately $27.5 million of outstanding debt pursuant to the Loan and Security Agreement and to repay approximately $0.5 million of outstanding debt pursuant to the Promissory Note. Upon the repayment of all amounts owed by the Company under these agreements, all commitments were terminated and all security interests granted by the Company were released.

In connection with the Term Loan Agreement entered into in December 2016, the Company issued to CRG four separate warrants to purchase a total of 528,958 shares of the Company’s common stock. The warrants are exercisable any time prior to December 30, 2026 at a price of $8.06 per share, with typical provisions for termination upon a change of control or a sale of all or substantially all of the assets of the Company. The warrants are classified within shareholders’ equity, and the proceeds were allocated between the debt and warrants based on their relative fair value. The fair value of the warrants was determined by the Black Scholes Merton option pricing model. The fair value of the warrants at issuance on December 30, 2016 was $1.8 million.

Equipment Lease Credit Facility

In October 2015, the Company signed a $10.0 million Credit Facility with Essex Capital Corporation (the “Lessor”) to fund capital equipment needs. As one of the conditions of the Term Loan Agreement, the Credit Facility is capped at a maximum of $5.0 million. Under the Credit Facility, Essex will fund capital equipment purchases presented by the Company. The Company will repay the amounts borrowed in 36 equal monthly installments from the date of the amount funded. At the end of the 36 month lease term, the Company has the option to (a) repurchase the leased equipment at the lesser of fair market value or 10% of the original equipment value, (b) extend the applicable lease for a specified period of time, which will not be less than one year, or (c) return the leased equipment to the Lessor.

In April 2016 and June 2016, the Company completed the first two draws under the Credit Facility, of $2.1 million and $2.5 million, respectively. The Company will make monthly payments of $67,000 under the first draw and $79,000 under the second draw. The borrowings under the Credit Facility are treated as capital leases. The amortization of the assets conveyed under the Credit Facility is included as a component of depreciation expense.

Shareholders' Equity	3 Months Ended
Shareholders' Equity	Mar. 31, 2017
Equity [Abstract]
Stockholders' Equity	Stockholders' Equity Private Investment in Public Equity Financing On September 21, 2016, Canon U.S.A., Inc. (“Canon”) became a related party when the Company sold 6,055,341 shares of its common stock (the “Canon Shares”) to Canon at $6.56 per share, the closing price on this date, for an aggregate cash purchase price of $39.7 million. As of September 21, 2016, the Canon Shares represented 19.9% of the outstanding shares of common stock of the Company. In connection with the sale of the Canon Shares, the Company agreed to grant Canon certain board designation rights, including the right to initially appoint a Class I director to the Company’s board of directors. On March 20, 2017, the Company filed with the Securities and Exchange Commission (the “SEC”) a registration statement on Form S-3 for purposes of registering the resale of the Canon Shares with the SEC.

- Definition

The entire disclosure for shareholders' equity comprised of portions attributable to the parent entity and noncontrolling interest, including other comprehensive income. Includes, but is not limited to, balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings, accumulated balance for each classification of other comprehensive income and amount of comprehensive income.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(d),(e))
-URI http://asc.fasb.org/extlink&oid=26873400&loc=d3e23780-122690

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21484-112644

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 310
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SAB TOPIC 4.E)
-URI http://asc.fasb.org/extlink&oid=27010918&loc=d3e74512-122707

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21488-112644

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.29-31)
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 4
-Subparagraph (SAB TOPIC 4.C)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187143-122770

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187085-122770

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 30
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6405834&loc=d3e23285-112656

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21475-112644

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Preferred Stock
-URI http://asc.fasb.org/extlink&oid=6521494

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21463-112644

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21564-112644

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section E

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section C

+ Details

Stock-Based Compensation

3 Months Ended

Mar. 31, 2017

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Stock-Based Compensation

Stock Incentive Plans

2006 Stock Incentive Plan

The Company’s 2006 Stock Option Plan (“2006 Plan”) was established for granting stock incentive awards to directors, officers, employees and consultants of the Company. Upon closing of the Company’s IPO in August 2014, the Company ceased granting stock incentive awards under the 2006 Plan. The 2006 Plan provided for the grant of incentive and non-qualified stock options and restricted stock grants as determined by the Company’s board of directors. Under the 2006 Plan, stock options were generally granted with exercise prices equal to or greater than the fair value of the common stock as determined by the board of directors, expired no later than 10 years from the date of grant, and vest over various periods not exceeding 4 years.

2014 Stock Incentive Plan

The Company’s 2014 Plan (“2014 Plan”, and together with the 2006 Plan, the “Stock Incentive Plans”), provides for the issuance of shares of common stock in the form of stock options, awards of restricted stock, awards of restricted stock units, performance awards, dividend equivalent awards, stock payment awards and stock appreciation rights to directors, officers, employees and consultants of the Company. Since the establishment of the 2014 Plan, the Company has only granted stock options. Generally, stock options are granted with exercise prices equal to or greater than the fair value of the common stock on the date of grant, expire no later than 10 years from the date of grant, and vest over various periods not exceeding 4 years.

The number of shares reserved for future issuance under the 2014 Plan is the sum of (1) 823,529 shares, (2) any shares that were granted under the 2006 Plan which are forfeited, lapsed unexercised or are settled in cash subsequent to the effective date of the 2014 Plan and (3) an annual increase on the first day of each calendar year beginning January 1, 2015 and ending on January 1, 2024, equal to the lesser of (A) 4% of the shares outstanding (on an as-converted basis) on the final day of the immediately preceding calendar year, and (B) such smaller number of shares determined by the Company’s Board of Directors. As of March 31, 2017 there were 973,512 shares available for future grant under the 2014 Plan.

Stock Options

During the three months ended March 31, 2017 and 2016, the Company granted stock options with an aggregate fair value of $1.7 million and $3.4 million, respectively, which are being amortized into compensation expense over the vesting period of the stock options as the services are being provided.

The following is a summary of stock option activity under the Plans (in thousands, except share and per share amounts):



	Number of Shares		Weighted-Average Exercise Price Per Share		Weighted-Average Remaining Contractual Term (In years)	Aggregate Intrinsic Value
Outstanding at December 31, 2016	4,042,627		$	8.20	7.05	$	4,091
Granted	498,450		5.68
Exercised	(111,630	)	3.03			328
Forfeited	(215,608	)	8.60
Cancelled	(61,574	)	15.35
Outstanding at March 31, 2017	4,152,265		7.91		7.28	3,841
Exercisable at March 31, 2017	2,267,596		6.99		5.92	3,726
Vested or expected to vest at March 31, 2017	3,881,040		7.88		7.15	3,836

Included in the stock options outstanding as of December 31, 2016 are 166,066 options to purchase common stock granted to certain executive officers of the Company that vest upon the achievement of certain performance conditions, which include the attainment of specified operating result and regulatory targets, by December 31, 2017, of which 20,000 options to purchase common stock upon the achievement of certain performance conditions were forfeited during the year ended December 31, 2016. There are 146,066 performance based stock options outstanding at March 31, 2017 and December 31, 2016. The Company will continually evaluate the probability of achievement of each performance condition and will commence recognition of stock-based compensation expense on these awards in the period the achievement of each performance condition is deemed probable, including a catch-up adjustment from the grant date.

The weighted‑average fair values of stock options granted in the three month periods ended March 31, 2017 and 2016 were $3.34 per share and $4.95 per share, respectively, and were calculated using the following estimated assumptions:



	Three months ended
	March 31,
	2017			2016
Weighted-average risk-free interest rate	2.02	%		1.52	%
Expected dividend yield	—	%		—	%
Expected volatility	63	%		60	%
Expected terms	6.0		years	6.0		years

The total fair values of stock options that vested during the three months ended March 31, 2017 and 2016 were $1.1 million and $1.3 million, respectively.

As of March 31, 2017, there was $7.4 million of total unrecognized compensation cost related to unvested stock options granted under the Stock Incentive Plans, including the unrecognized compensation expense of stock options with performance conditions deemed probable of vesting. Total unrecognized compensation cost will be adjusted for future changes in the estimated forfeiture rate. The Company expects to recognize that cost over a remaining weighted‑average period of 2.5 years as of March 31, 2017.

Restricted Stock Units

During the three months ended March 31, 2017, the Company awarded shares of restricted stock units to certain employees at no cost to them, which cannot be sold, assigned, transferred or pledged during the restriction period. The restricted stock and restricted stock units vest through the passage of time, assuming continued employment. Restricted stock units are not included in issued and outstanding common stock until the shares are vested and released. The fair value of the award at the time of the grant is expensed on a straight line basis. The granted restricted stock units had an aggregate fair value of $1.5 million, which are being amortized into compensation expense over the vesting period of the options as the services are being provided.

The following is a summary of restricted stock unit activity under the 2014 Plan (in thousands, except share and per share amounts):




	Number of Shares		Weighted-Average Grant Date Fair Value
Nonvested at December 31, 2016	272,195		5.83
Granted	249,925		5.85
Vested	—		—
Forfeited	(2,000	)	5.83
Canceled	—		—
Nonvested at March 31, 2017	520,120		5.84

There was no vesting of restricted stock units during the three months ended March 31, 2017. As of March 31, 2017, there was $2.3 million of total unrecognized compensation cost related to unvested stock options granted under the Stock Incentive Plans. Total unrecognized compensation cost will be adjusted for future changes in the estimated forfeiture rate. The Company expects to recognize that cost over a remaining weighted‑average period of 2.16 years as of March 31, 2017.

Employee Stock Purchase Plan

The Company’s 2014 Employee Stock Purchase Plan (the “2014 ESPP”) provides initially for granting up to 220,588 shares of the Company’s common stock to eligible employees. The 2014 ESPP plan period is semi-annual and allows participants to purchase the Company’s common stock at 85% of the lower of (i) the market value per share of common stock on the first day of the offering period or (ii) the market value per share of the common stock on the purchase date. Each participant can purchase up to a maximum of $25,000 per calendar year in fair market value. The first plan period began on August 7, 2014. Stock-based compensation expense from the 2014 ESPP was $62,000 and $53,000 for the three months ended March 31, 2017 and 2016, respectively. At March 31, 2017, there were 439,228 shares available under the 2014 ESPP.

Stock‑Based Compensation Expense

The following table summarizes the stock-based compensation expense resulting from awards granted under stock incentive plans, including the 2014 ESPP, that was recorded in the Company’s results of operations for the periods presented (in thousands):



	Three Months Ended March 31,
	2017		2016
Cost of product revenue	$	30	$	26
Research and development	302		270
Selling, general and administrative	796		968
Total stock-based compensation expense	$	1,128	$	1,264

As of March 31, 2017 and March 31, 2016, $29,000 and $26,000 of stock-based compensation expenses was capitalized as part of inventory or T2 instruments and components, respectively.

Net Loss Per Share

3 Months Ended

Mar. 31, 2017

Earnings Per Share [Abstract]

Net Loss Per Share

The following shares were excluded from the calculation of diluted net loss per share applicable to common stockholders, prior to the application of the treasury stock method, because their effect would have been anti‑dilutive for the periods presented:



	Three Months Ended March 31,
	2017	2016
Options to purchase common shares	4,152,265	3,887,285
Restricted stock units	520,120	—
Warrants to purchase common stock	528,958	—
Total	5,201,343	3,887,285

Co-Development Agreement	3 Months Ended
Co-Development Agreement	Mar. 31, 2017
Co-Development Agreements
Co-Development Agreement	Co-Development Agreements Canon US Life Sciences On September 21, 2016, Canon became a related party when the Company sold the Canon Shares for an aggregate cash purchase price of $39.7 million, which represented 19.9% of the outstanding shares of common stock of the Company. On February 3, 2015, the Company entered into a Co-Development Partnership Agreement (the “Co-Development Agreement”) with Canon U.S. Life Sciences, Inc. (“Canon US Life Sciences”) to develop a diagnostic test panel to rapidly detect Lyme disease. Under the terms of the Co-Development Agreement, the Company received an upfront payment of $2.0 million from Canon US Life Sciences, and the agreement includes an additional $6.5 million of consideration upon achieving certain development and regulatory milestones for total aggregate payments of up to $8.5 million. In October 2015, the Company achieved a specified technical requirement and received $1.5 million related to the achievement of the milestone. The Company is eligible to receive an additional $5.0 million under the arrangement, in two milestone payments of $2.0 million and $3.0 million, related to the achievement of additional development and regulatory milestones. All payments under the Co-Development Agreement are non-refundable once received. The Company will retain exclusive worldwide commercialization rights of any products developed under the Co-Development Agreement, including sales, marketing and distribution and Canon US Life Sciences will not receive any commercial rights and will be entitled to only receive royalty payments on the sales of all products developed under the Co-Development Agreement. Either party may terminate the Co-Development Agreement upon the occurrence of a material breach by the other party (subject to a cure period). The Company evaluated the deliverables under the Co-Development Agreement and determined that the Co-Development Agreement included one unit of accounting, the research and development services, as the joint research and development committee deliverable was deemed to be de minimis. The Company is recognizing revenue for research and development services as a component of research revenue in the condensed consolidated financial statements as the services are delivered using the proportional performance method of accounting, limited to payments earned. Costs incurred to deliver the services under the Co-Development Agreement are recorded as research and development expense in the condensed consolidated financial statements. The Company recorded revenue of $0.3 million and $0.5 million during the three months ended March 31, 2017 and 2016, respectively, under the Co-Development Agreement, and expects to record revenue over the next two years, provided development milestones are achieved. Allergan Sales, LLC On November 1, 2016, the Company entered into a Co-Development, Collaboration and Co-Marketing Agreement (the “Allergan Agreement”) with Allergan Sales, LLC (“Allergan Sales”) to develop (1) a direct detection diagnostic test panel that adds one additional bacteria species to the existing T2Bacteria product candidate (the “T2Bacteria II Panel”), and (2) a direct detection diagnostic test panel for testing drug resistance directly in whole blood (the “T2GNR Panel” and, together with the T2Bacteria II Panel, the “Developed Products”). In addition, both the Company and Allergan Sales will participate in a joint research and development committee and Allergan Sales will receive the right to cooperatively market the T2Candida, T2Bacteria, and the Developed Products under the Allergan Agreement to certain agreed-upon customers. Under the terms of the Allergan Agreement, the Company received an upfront payment of $2.0 million from Allergan Sales and will receive additional milestone payments upon achieving certain developmental milestones for total aggregate payments of up to $4.0 million. All payments under the Allergan Agreement are non-refundable once received. The Company will retain exclusive worldwide commercialization rights of any products developed under the Allergan Agreement, including distribution, subject to Allergan Sales’ right to co-market the Developed Products. Allergan Sales, at its election, may co-market T2Candida, T2Bacteria and the Developed Products worldwide to certain agreed-upon customers and will receive royalty based on its sales for a period of time. The Company evaluated the deliverables under the Allergan Agreement and determined that the Allergan Agreement included two units of accounting, the research and development services for the T2Bacteria II Panel and the research and development services for the T2GNR Panel, as the joint research and development committee and right to cooperatively market deliverables were deemed to be de minimus. The Company is recognizing revenue for research and development services as a component of research revenue in the consolidated financial statements as the services are delivered using the proportional performance method of accounting, limited to payments earned. Costs incurred to deliver the services under the Allergan Agreement are recorded as research and development expense in the consolidated financial statements. The Company recorded revenue of $38,000 for the three months ended March 31, 2017 under the Allergan Agreement and expects to record revenue over the next two years, provided development and regulatory milestones are achieved.

Summary of Significant Accounting Policies (Policies)	3 Months Ended
Summary of Significant Accounting Policies (Policies)	Mar. 31, 2017
Accounting Policies [Abstract]
Basis of Presentation	Basis of Presentation The Company’s financial statements have been prepared in conformity with generally accepted accounting principles in the United States of America (“GAAP”). Any reference in these notes to applicable guidance is meant to refer to the authoritative United States GAAP as defined in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASU”) of the Financial Accounting Standards Board (“FASB”). The Company’s condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiary, T2 Biosystems Securities Corporation. All intercompany balances and transactions have been eliminated.
Unaudited Interim Financial Information	Unaudited Interim Financial Information Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. Accordingly, these interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016. The accompanying interim condensed consolidated balance sheet as of March 31, 2017, the condensed consolidated statements of operations and comprehensive loss for the three months ended March 31, 2017 and 2016, the condensed consolidated statements of cash flows for the three months ended March 31, 2017 and 2016 and the related financial data and other information disclosed in these notes are unaudited. The unaudited interim financial statements have been prepared on the same basis as the audited annual financial statements, and, in the opinion of management, reflect all adjustments, consisting of normal recurring adjustments, necessary for the fair presentation of the Company’s financial position as of March 31, 2017, and the results of its operations and its cash flows for the three months ended March 31, 2017 and 2016. The results for the three months ended March 31, 2017 are not necessarily indicative of the results to be expected for the year ending December 31, 2017, any other interim periods, or any future year or period.
Segment Information	Segment Information Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision maker, or decision‑making group, in deciding how to allocate resources and in assessing performance. The Company’s chief operating decision maker is the Chief Executive Officer. The Company views its operations and manages its business in one operating segment, which is the business of developing and, upon regulatory clearance, launching commercially its diagnostic products aimed at lowering mortality rates, improving patient outcomes and reducing the cost of healthcare by helping medical professionals make targeted treatment decisions earlier.
Net Loss Per Share	Net Loss Per Share Basic net loss per share is calculated by dividing net loss by the weighted-average number of shares of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is calculated by adjusting the weighted-average number of shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury-stock method. For purposes of the diluted net loss per share calculation, stock options and unvested restricted stock are considered to be common stock equivalents, but have been excluded from the calculation of diluted net loss per share, as their effect would be anti-dilutive for all periods presented. Therefore, basic and diluted net loss per share applicable to common stockholders was the same for all periods presented.
Guarantees	Guarantees As permitted under Delaware law, the Company indemnifies its officers and directors for certain events or occurrences while each such officer or director is, or was, serving at the Company’s request in such capacity. The term of the indemnification is the officer’s or director’s lifetime. The maximum potential amount of future payments the Company could be required to make is unlimited; however, the Company has directors’ and officers’ liability insurance coverage that limits its exposure and enables the Company to recover a portion of any future amounts paid. The Company leases office, laboratory and manufacturing space under noncancelable operating leases. The Company has standard indemnification arrangements under the leases that require it to indemnify the landlords against all costs, expenses, fines, suits, claims, demands, liabilities, and actions directly resulting from any breach, violation or nonperformance of any covenant or condition of the Company’s leases. In the ordinary course of business, the Company enters into indemnification agreements with certain suppliers and business partners where the Company has certain indemnification obligations limited to the costs, expenses, fines, suits, claims, demands, liabilities and actions directly resulting from the Company’s gross negligence or willful misconduct, and in certain instances, breaches, violations or nonperformance of covenants or conditions under the agreements. As of March 31, 2017 and December 31, 2016, the Company had not experienced any material losses related to these indemnification obligations, and no material claims with respect thereto were outstanding. The Company does not expect significant claims related to these indemnification obligations and, consequently, concluded that the fair value of these obligations is negligible, and no related reserves were established.
Revenue Recognition	Revenue Recognition The Company generates revenue from product sales, which includes the sale of instruments, consumable diagnostic tests and related services, and research and development agreements with third parties. The Company recognizes revenue in accordance with FASB ASC Topic 605, Revenue Recognition (“ASC 605”). Accordingly, the Company recognizes revenue when all of the following criteria have been met: i. Persuasive evidence of an arrangement exists ii. Delivery has occurred or services have been rendered iii. The seller’s price to the buyer is fixed or determinable iv. Collectability is reasonably assured If any of the above criteria have not been met, the Company defers revenue until such time each of the criteria have been satisfied. Product revenue is generated by the sale of instruments and consumable diagnostic tests predominantly through the Company's direct sales force in the United States and distributors in geographic regions outside the United States. The Company does not offer product return or exchange rights (other than those relating to defective goods under warranty) or price protection allowances to its customers, including its distributors. Payment terms granted to distributors are the same as those granted to end-user customers and payments are not dependent upon the distributors’ receipt of payment from their end-user customers. The Company either sells instruments to customers and international distributors, or retains title and places the instrument at the customer site pursuant to a reagent rental agreement. When the instrument is directly purchased by a customer, the Company recognizes revenue when all applicable revenue recognition criteria are met. When the instrument is placed under a reagent rental agreement, the Company’s customers generally agree to fixed term agreements, which can be extended, certain of which may include minimum purchase commitments and/or incremental charges on each consumable diagnostic test purchased, which varies based on the volume of test cartridges purchased. Revenue from the sale of consumable diagnostic tests, which includes the incremental charge, is recognized upon delivery as a component of product revenue in the Company’s consolidated statements of operations and comprehensive loss. Direct sales of instruments include warranty, maintenance and technical support services for one year following the installation of the purchased instrument (“Maintenance Services”). After the completion of the initial Maintenance Services period, customers have the option to renew the Maintenance Services for additional one year periods in exchange for additional consideration. In addition, the Company may provide training to customers. The Company defers revenue from the initial sale of the instrument equal to the relative fair value of the one year of Maintenance Services and training and recognizes the amounts ratably over the service delivery period. The Company warrants that consumable diagnostic tests will be free from defects, when handled according to product specifications, for the stated life of the product. To fulfill valid warranty claims, the Company either provides a credit to its customers on future orders or provides a replacement product. Accordingly, the Company defers revenue associated with the estimated defect rates of the consumable diagnostic tests. The Company does not offer rights of return for instruments or consumable diagnostic tests. Shipping and handling costs incurred associated with products sold to customers are recorded as a cost of product revenue in the consolidated statement of operations and comprehensive loss. Shipping and handling costs billed to customers in connection with a product sale are recorded as a component of product revenue in the consolidated statements of operations and comprehensive loss. For multiple-element arrangements, the Company identifies the deliverables included within each agreement and evaluates which deliverables represent separate units of accounting. The determination that multiple elements in an arrangement meet the criteria for separate units of accounting requires the Company’s management to exercise judgment. The Company accounts for those components as separate elements when the following criteria are met: (1) the delivered items have value to the customer on a stand-alone basis; and, (2) if there is a general right of return relative to the delivered items, delivery or performance of the undelivered items is considered probable and within its control. The consideration received is allocated among the separate units of accounting based on a selling price hierarchy. The selling price hierarchy is based on: (1) vendor specific objective evidence (“VSOE”), if available; (2) third party evidence of selling price if VSOE is not available; or (3) best estimated selling price (“BESP”) if neither VSOE nor third party evidence is available. The Company generally expects that it will not be able to establish selling price using third-party evidence due to the nature of our products and the markets in which the Company competes, and, as such, the Company typically will determine selling price using VSOE or BESP. When the Company establishes selling price using BESP, consideration is given to both market and Company-specific factors, including the cost to produce the deliverable and the anticipated margin on that deliverable, as well as the characteristics of markets in which the deliverable is sold. Revenue earned from activities performed pursuant to research and development agreements is reported as research revenue in the consolidated statements of operations and comprehensive loss, using the proportional performance method as the work is completed, limited to payments earned, and the related costs are expensed as incurred as research and development expense. The timing of receipt of cash from the Company’s research and development agreements generally differs from when revenue is recognized.
Product Recall	Product Recall In July 2016, the Company initiated a voluntary recall and replacement of its T2Candida cartridges at certain customer sites because T2Candida was experiencing higher than normal invalid test rates as the T2Candida cartridges aged. As of June 30, 2016, as a result of this voluntary recall, the Company deferred revenue totaling $0.1 million and recorded additional costs of product revenue of $41,000 related to returned products, which are no longer usable. As of March 31, 2017, the Company had $37,000 of deferred revenue and $2,000 of warranty reserve remaining, both related to this voluntary recall. The impact of the voluntary recall on T2Candida cartridges in inventory was not material to the condensed consolidated financial statements.
Cost of Product Revenue	Cost of Product Revenue Cost of product revenue includes the cost of materials, direct labor and manufacturing overhead costs used in the manufacture of consumable diagnostic tests sold to customers and related license and royalty fees. Cost of product revenue also includes depreciation on revenue generating T2Dx that have been placed with customers under reagent rental agreements; costs of materials, direct labor and manufacturing overhead costs on the T2Dx sold to customers; and other costs such as customer support costs, royalties and license fees, warranty and repair and maintenance expense on the T2Dx that have been placed with customers under reagent rental agreements.
Research and Development Costs	Research and Development Costs Costs incurred in the research and development of the Company’s product candidates are expensed as incurred. Research and development expenses consist of costs incurred in performing research and development activities, including activities associated with performing services under research revenue arrangements, and include salaries and benefits, stock compensation, research‑related facility and overhead costs, laboratory supplies, equipment and contract services.
Recent Accounting Pronouncements	Recent Accounting Standards From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption. Accounting Standards Adopted In July 2015, the FASB issued ASU No. 2015-11, Inventory (Topic 330): Simplifying the Measurement of Inventory (“ASU 2015-11”). The standard simplifies the subsequent measurement of inventory by requiring inventory to be measured at the lower of cost and net realizable value for entities using the first-in-first out method of valuing inventory. ASU 2015-11 eliminates other measures required by current guidance to determine net realizable value. ASU 2015-11 is effective for fiscal years beginning after December 15, 2016 and interim periods within those fiscal years and early adoption is permitted. The Company's adoption of this standard did not have a material effect on its condensed consolidated financial statements. In March 2016, the FASB released ASU No. 2016-09 Improvements to Employee Share-Based Payment Accounting (“ASU 2016-09”) which is intended to simplify income tax accounting for excess tax benefits, accounting for forfeitures, and employer statutory withholding. Under the current guidance, excess tax benefits that result from an award vesting or settling are recognized in additional paid-in capital in the period that they reduce cash taxes payable. This requires the provision to be computed on a with and without option basis and may result in net operating loss and credit carryforwards on the balance sheet being less than what is available on the tax return. Under the new guidance, the income tax effects of awards will be recognized as a component of income tax expense when the awards vest or are settled (regardless if cash taxes are reduced). For interim reporting purposes, companies will account for excess tax benefits and tax deficiencies as discrete items in the period during which they occurred. The guidance is effective for public entities for fiscal years beginning after December 15, 2016, and interim periods within those years. Early adoption is permitted, however all of the guidance included in the update must be applied when adopted. The Company must use a modified retrospective transition method for adopting and record the cumulative effect of all unrecognized benefits and any change in valuation allowances at the end of the prior tax period as an adjustment to retained earnings. The Company's adoption of this standard did not have a material effect on its condensed consolidated financial statements and prior periods have not been adjusted. As a result, the Company established a net operating loss deferred tax asset of $1.2 million to account for prior period excess tax benefits through retained earnings, however an offsetting valuation allowance of $1.2 million will also be established through retained earnings because it is not more likely than not that the deferred tax asset will be realized due to historical and expected future losses, such that there is no impact on the Company’s condensed consolidated financial statements. The Company also elected to maintain the use of estimated forfeitures in the calculation of stock based compensation. In March 2016, the FASB issued ASU No. 2016-06, Derivatives and Hedging (Topic 815): Contingent Put and Call Options in Debt Instruments (“ASU 2016-06”), which applies to all issuers of or investors in debt instruments with embedded call or put options. ASU 2016-06 clarifies the requirements for assessing whether contingent call or put options that can accelerate the payment of principal on debt instruments are clearly and closely related to their debt hosts. Entities performing the assessment under the guidance of ASU 2016-06 are required to assess the embedded call or put options solely in accordance with the four-step decision process. In addition, ASU 2016-06 clarifies what steps are required when assessing whether the economic characteristics and risks of call or put options are clearly and closely related to the economic characteristics and risks of their debt hosts. ASU 2016-06 is effective for financial statements issued for fiscal years beginning after December 15, 2016 and interim periods within those fiscal years using the modified retrospective method for existing debt instruments. The Company's adoption of this standard did not have a material effect on its condensed consolidated financial statements. Accounting Standards Issued, Not Adopted In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments ("ASC 2016-15"), which provides guidance on the classification of certain specific cash flow issues including debt prepayment or extinguishment costs, settlement of certain debt instruments, contingent consideration payments made after a business combination, proceeds from the settlement of certain insurance claims and distributions received from equity method investees. The standard requires the use of a retrospective approach to all periods presented, but may be applied prospectively if retrospective application would be impracticable. The guidance is effective for public entities for fiscal years beginning after December 15, 2017, and interim periods within those years, and early application is permitted. The Company is currently evaluating the impact of its pending adoption of ASU 2016-15 on the Company’s consolidated financial statements. In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which applies to all leases. Under ASU 2016-02, a right-of-use asset and lease obligation will be recorded for all leases, whether operating or financing leases, while the statement of operations will reflect lease expense for operating leases and amortization and interest expense for financing leases. ASU 2016-02 is effective for fiscal years beginning after December 15, 2018 and interim periods within those years, which is the year ended December 31, 2019 for the Company. Entities are required to use a modified retrospective approach of adoption for leases that exist or are entered into after the beginning of the earliest comparative period in the financial statements. Full retrospective application is prohibited. The Company is evaluating the new guidance and the expected effect on the Company’s consolidated financial statements. In June 2014, the FASB issued amended guidance, ASU No. 2014-09, Revenue from Contracts with Customers (“ASU 2014-09”), which is applicable to revenue recognition that will now be effective for the Company for the year ending December 31, 2018, as a result of the deferral of the effective date adopted by the FASB in July 2015. The new guidance must be adopted using either a full retrospective approach for all periods presented or a modified retrospective approach. Early adoption prior to the original adoption date of ASU 2014-09 is not permitted. The new guidance applies a more principles-based approach to revenue recognition. The Company currently anticipates adoption of the new standard effective January 1, 2018 under the full retrospective method. The Company’s revenue is primarily comprised of product sales and research services, and the Company is in the process of determining the impact of the new standard on its financial statements.

Fair Value Measurements (Tables)

3 Months Ended

Mar. 31, 2017

Fair Value Disclosures [Abstract]

Schedule of financial assets and liabilities at fair value on a recurring basis



	Balance at December 31, 2017		Quoted Prices in Active Markets for Identical Assets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Assets:
Cash	$	6,702	$	6,702	$	—	$	—
Money market funds	52,120		52,120		—		—
Restricted cash	260		260		—		—
Total	$	59,082	$	59,082	$	—	$	—



	Balance at December 31, 2016		Quoted Prices in Active Markets for Identical Assets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Assets:
Cash	$	16,887	$	16,887	$	—	$	—
Money market funds	56,601		56,601		—		—
Restricted cash	260		260		—		—
Total	$	73,748	$	73,748	$	—	$	—

Supplemental Balance Sheet Information (Tables)

3 Months Ended

Mar. 31, 2017

Balance Sheet Related Disclosures [Abstract]

Schedule of inventory

Inventories are stated at the lower of cost or net realizable value on a first-in, first-out basis and are comprised of the following (in thousands):



	March 31, 2017		December 31, 2016
Raw materials	$	215	$	389
Work-in-process	262		351
Finished goods	12		63
Total inventories, net	$	489	$	803

Schedule of property and equipment

Property and equipment consists of the following (in thousands):



	March 31, 2017			December 31, 2016
Office and computer equipment	$	409		$	409
Software	743			708
Laboratory equipment	4,562			4,516
Furniture	200			200
Manufacturing equipment	910			897
Manufacturing tooling and molds	154			154
T2-owned instruments and components	10,522			9,119
Leasehold improvements	3,353			3,353
Construction in progress	1,343			1,299
	22,196			20,655
Less accumulated depreciation and amortization	(7,728		)	(7,066		)
Property and equipment, net	$	14,468		$	13,589

Components of accrued expenses

Accrued expenses consist of the following (in thousands):



	March 31, 2017		December 31, 2016
Accrued payroll and compensation	$	1,848	$	2,479
Accrued research and development expenses	724		846
Accrued professional services	915		884
Other accrued expenses	573		699
Total accrued expenses	$	4,060	$	4,908

Stock-Based Compensation (Tables)

3 Months Ended

Mar. 31, 2017

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Summary of stock option activity

The following is a summary of stock option activity under the Plans (in thousands, except share and per share amounts):



	Number of Shares		Weighted-Average Exercise Price Per Share		Weighted-Average Remaining Contractual Term (In years)	Aggregate Intrinsic Value
Outstanding at December 31, 2016	4,042,627		$	8.20	7.05	$	4,091
Granted	498,450		5.68
Exercised	(111,630	)	3.03			328
Forfeited	(215,608	)	8.60
Cancelled	(61,574	)	15.35
Outstanding at March 31, 2017	4,152,265		7.91		7.28	3,841
Exercisable at March 31, 2017	2,267,596		6.99		5.92	3,726
Vested or expected to vest at March 31, 2017	3,881,040		7.88		7.15	3,836

Schedule of estimated assumptions used to calculate weighted-average fair value of options granted



	Three months ended
	March 31,
	2017			2016
Weighted-average risk-free interest rate	2.02	%		1.52	%
Expected dividend yield	—	%		—	%
Expected volatility	63	%		60	%
Expected terms	6.0		years	6.0		years

Schedule of nonvested restricted stock units activity

The following is a summary of restricted stock unit activity under the 2014 Plan (in thousands, except share and per share amounts):




	Number of Shares		Weighted-Average Grant Date Fair Value
Nonvested at December 31, 2016	272,195		5.83
Granted	249,925		5.85
Vested	—		—
Forfeited	(2,000	)	5.83
Canceled	—		—
Nonvested at March 31, 2017	520,120		5.84

Summary of stock-based compensation expense for stock options granted that was recorded in the Company's results of operations



	Three Months Ended March 31,
	2017		2016
Cost of product revenue	$	30	$	26
Research and development	302		270
Selling, general and administrative	796		968
Total stock-based compensation expense	$	1,128	$	1,264

Net Loss Per Share Net Loss Per Share (Tables)

3 Months Ended

Mar. 31, 2017

Earnings Per Share [Abstract]

Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share



	Three Months Ended March 31,
	2017	2016
Options to purchase common shares	4,152,265	3,887,285
Restricted stock units	520,120	—
Warrants to purchase common stock	528,958	—
Total	5,201,343	3,887,285

Nature of Business (Details) - USD ($) $ in Thousands	3 Months Ended
Nature of Business (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016	Mar. 31, 2016	Dec. 31, 2015
Debt Instrument
Cash and cash equivalents	$ 58,822	$ 73,488	$ 59,519	$ 73,662
Accumulated deficit	$ (218,392)	$ (203,689)
Minimum
Debt Instrument
Period over which cash resources will be sufficient to allow Company to fund current operating plan	12 months
Loan And Security Agreement \| Equipment lease facility \| Maximum
Debt Instrument
Remaining borrowing capacity	$ 1,500

Summary of Significant Accounting Policies (Details)	3 Months Ended
Summary of Significant Accounting Policies (Details)	Mar. 31, 2017 segment
Segment Information
Number of operating segments	1

Summary of Significant Accounting Policies Product Service (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Mar. 31, 2017	Mar. 31, 2016	Jun. 30, 2016	Dec. 31, 2016
Product information
Deferred revenue	$ 2,127			$ 2,445
Costs of product revenue	$ 1,627	$ 1,026
T2Dx
Product information
Maintenance Services period (in years)	1 year
Additional period for Maintenance Service option (in years)	1 year
T2Candida
Product information
Deferred revenue	$ 37		$ 100
Costs of product revenue			$ 41
Remaining warranty reserve	$ 2

Summary of Significant Accounting Policies Recent Accounting Pronouncements (Details) $ in Millions	Mar. 31, 2017 USD ($)
Accounting Standards Update 2016-09, Excess Tax Benefit Component \| Retained Earnings
New Accounting Pronouncement, Early Adoption [Line Items]
Cumulative effect of new accounting principle in period of adoption	$ 1.2

Fair Value Measurements (Details) - Recurring - Total - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Assets:
Restricted cash	$ 260	$ 260
Total assets	59,082	73,748
Cash
Assets:
Cash and cash equivalents	6,702	16,887
Money market funds
Assets:
Cash and cash equivalents	52,120	56,601
Level I
Assets:
Restricted cash	260	260
Total assets	59,082	73,748
Level I \| Cash
Assets:
Cash and cash equivalents	6,702	16,887
Level I \| Money market funds
Assets:
Cash and cash equivalents	52,120	56,601
Level 2
Assets:
Restricted cash	0	0
Total assets	0	0
Level 2 \| Cash
Assets:
Cash and cash equivalents	0	0
Level 2 \| Money market funds
Assets:
Cash and cash equivalents	0	0
Level 3
Assets:
Restricted cash	0	0
Total assets	0	0
Level 3 \| Cash
Assets:
Cash and cash equivalents	0	0
Level 3 \| Money market funds
Assets:
Cash and cash equivalents	$ 0	$ 0

Supplemental Balance Sheet Information - Inventories (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Balance Sheet Related Disclosures [Abstract]
Raw materials	$ 215	$ 389
Work-in-process	262	351
Finished goods	12	63
Total inventories, net	$ 489	$ 803

Supplemental Balance Sheet Information - Property and Equipment - (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016	Dec. 31, 2016
Property and Equipment
Property and equipment, gross	$ 22,196		$ 20,655
Accumulated depreciation and amortization	(7,728)		(7,066)
Property and equipment, net	14,468		13,589
Office and computer equipment
Property and Equipment
Property and equipment, gross	409		409
Software
Property and Equipment
Property and equipment, gross	743		708
Laboratory equipment
Property and Equipment
Property and equipment, gross	4,562		4,516
Furniture
Property and Equipment
Property and equipment, gross	200		200
Manufacturing equipment
Property and Equipment
Property and equipment, gross	910		897
Manufacturing tooling and molds
Property and Equipment
Property and equipment, gross	154		154
T2-owned instruments and components
Property and Equipment
Property and equipment, gross	10,522		9,119
Leasehold improvements
Property and Equipment
Property and equipment, gross	3,353		3,353
Construction in progress
Property and Equipment
Property and equipment, gross	1,343		1,299
T2 Owned Instruments in Service
Property and Equipment
Property and equipment, gross	$ 6,700		$ 5,700
Estimated useful lives (in years)	5 years
Depreciation expense recorded as a component of cost of product revenue	$ 200	$ 100

Supplemental Balance Sheet Information - Accrued Expenses (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Accrued expenses
Accrued payroll and compensation	$ 1,848	$ 2,479
Accrued research and development expenses	724	846
Accrued professional services	915	884
Other accrued expenses	573	699
Total accrued expenses	$ 4,060	$ 4,908

Notes Payable - Schedule of Debt (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Debt Instrument
Total notes payable	$ 41,066	$ 40,773
Less: current portion of notes payable	(1,316)	(1,269)
Notes payable, net of current portion	39,750	39,504
Medium-term Notes \| Term Loan Agreement
Debt Instrument
Total notes payable	37,624	37,031
Deferred issuance costs	2,900	3,000
Line of Credit \| Equipment Lease Credit Facility
Debt Instrument
Total notes payable	3,442	3,742
Deferred issuance costs	$ 40	$ 45

Notes Payable - Term Loan Agreement (Details) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended
	Dec. 31, 2016 USD ($) warrant $ / shares shares	Mar. 31, 2017 USD ($)	Mar. 31, 2016 USD ($)
Debt Instrument
Repayments of note payable		$ 299	$ 80
Loan And Security Agreement
Debt Instrument
Repayments of note payable	$ 27,500
Promissory Note
Debt Instrument
Repayments of note payable	500
CRG Servicing LLC \| Term Loan Agreement
Debt Instrument
Proceeds from issuance of long-term debt	40,000
Line of credit, additional borrowing capacity	$ 10,000
Debt term (in years)	6 years
Debt instrument, term of interest-only payments (in years)	3 years
Debt instrument, extended term interest only payments (in years)	4 years
Final fee as a percentage of the principal outstanding (as a percent)	8.00%
Debt instrument, prepayment fee term (in years)	5 years
Additional interest rate, event of default (as a percent)	4.00%
Proceeds from issuance of note payable, net	$ 39,200
Portion of proceeds used for debt repayment	$ 28,000
Number of warrants \| warrant	4
Prior to Approval Milestone \| CRG Servicing LLC \| Term Loan Agreement
Debt Instrument
Annual fixed rate (as a percent)	12.50%
Deferred interest rate (as a percent)	4.00%
Following Approval Milestone \| CRG Servicing LLC \| Term Loan Agreement
Debt Instrument
Annual fixed rate (as a percent)	11.50%
Deferred interest rate (as a percent)	3.50%
Common stock
Debt Instrument
Number of warrants \| warrant	4
Number of shares issuable for warrants outstanding (in shares) \| shares	528,958
Exercise price of warrants (in dollars per share) \| $ / shares	$ 8.06
Fair market value of warrants	$ 1,800

Notes Payable - Equipment Lease Credit Facility (Details) - Equipment lease facility	1 Months Ended
	Jun. 30, 2016 USD ($) draw	Apr. 30, 2016 USD ($)	Oct. 31, 2015 USD ($)
Equipment Lease Credit Facility
Capital lease obligation
Initial borrowing capacity			$ 10,000,000
Maximum borrowings available (up to)			$ 5,000,000
Debt term (in months)			36 months
Repurchase price as percentage of original equipment value that the equipment under lease may be repurchased by lessee			10.00%
Minimum lease period to extend lease (in years)			1 year
Number of draws \| draw	2
First Draw
Capital lease obligation
Amount of draw		$ 2,100,000
Amount of monthly payment		$ 67,000
Second Draw
Capital lease obligation
Amount of draw	$ 2,500,000
Amount of monthly payment	$ 79,000

Shareholders' Equity (Details) - Private Placement $ / shares in Units, $ in Millions	Sep. 21, 2016 USD ($) $ / shares shares
Class of Stock [Line Items]
Number of shares sold \| shares	6,055,341
Sale price of stock (in dollars per share) \| $ / shares	$ 6.56
Proceeds from private investment in public equity \| $	$ 39.7
Percentage of common shares outstanding (as a percentage)	19.90%

Stock-Based Compensation (Details) - USD ($)	3 Months Ended		12 Months Ended
Stock-Based Compensation (Details) - USD ($)	Mar. 31, 2017	Mar. 31, 2016	Dec. 31, 2016	Mar. 31, 2017	Dec. 31, 2014
Share-Based Compensation
Fair value of vested stock options	$ 1,100,000	$ 1,300,000
Unrecognized compensation cost related to unvested stock options				$ 7,400,000
Weighted-average period (in years)	2 years 6 months 11 days
Stock-based compensation expense	$ 1,128,000	1,264,000
Performance-based awards
Share-Based Compensation
Remaining performance stock based options (in shares)	146,066		146,066	146,066
Number of Shares
Outstanding, beginning of the period (in shares)	146,066
Outstanding, end of the period (in shares)	146,066		146,066
2006 and 2014 Stock Option Plans \| Stock Option
Share-Based Compensation
Aggregate fair value of options granted	$ 1,700,000	$ 3,400,000
Remaining performance stock based options (in shares)	4,042,627		4,042,627	4,152,265
Forfeited performance stock based options (in shares)	215,608
Number of Shares
Outstanding, beginning of the period (in shares)	4,042,627
Granted (in shares)	498,450
Exercised (in shares)	(111,630)
Forfeited (in shares)	(215,608)
Cancelled (in shares)	(61,574)
Outstanding, end of the period (in shares)	4,152,265		4,042,627
Exercisable (in shares)				2,267,596
Vested or expected to vest (in shares)				3,881,040
Weighted Average Exercise Price Per Share
Outstanding, beginning of the period (in dollars per share)	$ 8.20
Granted (in dollars per share)	5.68
Exercised (in dollars per share)	3.03
Forfeited (in dollars per share)	8.60
Cancelled (in dollars per share)	15.35
Outstanding, end of the period (in dollars per share)	$ 7.91		$ 8.20
Exercisable (in dollars per share)				$ 6.99
Vested or expected to vest (in dollars per share)				$ 7.88
Weighted-Average Remaining Contractual Term (in years)
Outstanding (in years)	7 years 3 months 11 days		7 years 18 days
Exercisable (in years)	5 years 11 months 1 day
Vested or expected to vest (in years)	7 years 1 month 24 days
Aggregate Intrinsic Value
Outstanding, beginning of the period	$ 4,091,000
Exercised (in dollars)	328,000
Outstanding, end of the period	$ 3,841,000		$ 4,091,000
Exercisable				$ 3,726,000
Vested or expected to vest				$ 3,836,000
Fair value assumptions
Weighted average fair value of options granted (in dollars per share)	$ 3.34	$ 4.95
Weighted-average risk-free interest rate (as a percentage)	2.02%	1.52%
Expected dividend yield (as a percentage)	0.00%	0.00%
Expected volatility (as a percentage)	63.00%	60.00%
Expected terms (in years)	6 years	6 years
2006 Stock Option Plan \| Maximum \| Stock Option
Share-Based Compensation
Expiration period (in years)	10 years
Vesting period (in years)	4 years
2014 Stock Option Plan \| Stock Option
Share-Based Compensation
Shares available for future issuance under stock incentive plan (in shares)				823,529
Percentage of common shares outstanding (as a percentage)				4.00%
Shares available for grant (in shares)				973,512
2014 Stock Option Plan \| Maximum \| Stock Option
Share-Based Compensation
Expiration period (in years)	10 years
Vesting period (in years)	4 years
2014 ESPP \| Employee Stock Purchase Plan
Share-Based Compensation
Shares available for grant (in shares)				439,228	220,588
Percentage of full share price paid in purchase of common stock	85.00%
Maximum amount of annual employee common stock purchases	$ 25,000
Stock-based compensation expense	$ 62,000	$ 53,000
Executive Officer \| Performance-based awards
Share-Based Compensation
Remaining performance stock based options (in shares)	166,066		166,066
Forfeited performance stock based options (in shares)			20,000
Number of Shares
Outstanding, beginning of the period (in shares)	166,066
Forfeited (in shares)			(20,000)
Outstanding, end of the period (in shares)			166,066

Stock-Based Compensation Restricted Stock Unit Activity (Details) $ / shares in Units, $ in Millions	3 Months Ended
	Mar. 31, 2017 USD ($) $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Weighted-average period (in years)	2 years 6 months 11 days
Restricted Stock Units
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Unvested restricted shares at the beginning of the period \| shares	272,195
Restricted shares granted \| shares	249,925
Restricted shares vested \| shares	0
Restricted shares forfeited \| shares	(2,000)
Unvested restricted shares at the end of the period \| shares	520,120
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Unvested restricted shares at the beginning of the period (USD per share) \| $ / shares	$ 5.83
Granted (USD per share) \| $ / shares	5.85
Vested (USD per share) \| $ / shares	0.00
Forfeited (USD per share) \| $ / shares	5.83
Unvested restricted shares at the end of the period (USD per share) \| $ / shares	$ 5.84
Granted restricted stock fair value \| $	$ 1.5
Unrecognized compensation cost \| $	$ 2.3
Weighted-average period (in years)	2 years 1 month 28 days

Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Stock-based compensation expense
Stock-based compensation expense	$ 1,128	$ 1,264
T2 Owned Instruments in Service
Stock-based compensation expense
Stock-based compensation expense	29	26
Cost of product revenue
Stock-based compensation expense
Stock-based compensation expense	30	26
Research and development
Stock-based compensation expense
Stock-based compensation expense	302	270
Selling, general and administrative
Stock-based compensation expense
Stock-based compensation expense	$ 796	$ 968

Warrants (Details) - Common stock $ / shares in Units, $ in Millions	1 Months Ended
	Dec. 31, 2016 USD ($) warrant $ / shares shares
Class of Warrant or Right [Line Items]
Number of warrants \| warrant	4
Number of shares issuable for warrants outstanding (in shares) \| shares	528,958
Exercise price of warrants (in dollars per share) \| $ / shares	$ 8.06
Fair market value of warrants \| $	$ 1.8

Net Loss Per Share (Details) - shares	3 Months Ended
Net Loss Per Share (Details) - shares	Mar. 31, 2017	Mar. 31, 2016
Antidilutive Securities
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)	5,201,343	3,887,285
Stock Option
Antidilutive Securities
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)	4,152,265	3,887,285
Restricted Stock Units
Antidilutive Securities
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)	520,120	0
Warrant
Antidilutive Securities
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)	528,958	0

Co-Development Agreement (Details) $ in Thousands				1 Months Ended	3 Months Ended
Co-Development Agreement (Details) $ in Thousands	Nov. 01, 2016 USD ($) specie	Sep. 21, 2016 USD ($)	Feb. 03, 2015 USD ($) item	Oct. 31, 2015 USD ($)	Mar. 31, 2017 USD ($) item	Mar. 31, 2016 USD ($)
Co-Development Agreement
Revenues					$ 941	$ 1,096
Co Development Partnership Agreement \| Canon U.S. Life Sciences Inc.
Co-Development Agreement
Upfront payment			$ 2,000
Additional consideration receivable upon achievement of certain development and regulatory milestones			6,500
Aggregate consideration receivable			$ 8,500
Proceeds received for achievement of milestone				$ 1,500
Additional consideration receivable upon achievement of additional development and regulatory milestones					$ 5,000
Number of milestone payments \| item					2
Additional consideration receivable upon achievement of development and regulatory milestones, payment one					$ 2,000
Additional consideration receivable upon achievement of development and regulatory milestones, payment two					3,000
Number of units \| item			1
Revenues					300	$ 500
Co Development Partnership Agreement \| Allergan Sales
Co-Development Agreement
Upfront payment	$ 2,000
Aggregate consideration receivable	$ 4,000
Revenues					$ 38
Number of additional bacteria species added to existing product candidate \| specie	1
Private Placement
Co-Development Agreement
Proceeds from sale of shares in related party		$ 39,700
Percentage of outstanding shares at date of sale		19.90%

Warrants	3 Months Ended
Warrants	Mar. 31, 2017
Equity [Abstract]
Warrants	Warrants In connection with the Term Loan Agreement entered into in December 2016, the Company issued to CRG four separate warrants to purchase a total of 528,958 shares of the Company’s common stock. The warrants are exercisable any time prior to December 30, 2026 at a price of $8.06 per share, with typical provisions for termination upon a change of control or a sale of all or substantially all of the assets of the Company. The warrants are classified within shareholders’ equity, and the proceeds were allocated between the debt and warrants based on their relative fair value. The fair value of the warrants was determined by the Black‑Scholes‑Merton option pricing model. The fair value of the warrants at issuance on December 30, 2016 was $1.8 million.