CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $) In Thousands, unless otherwise specified	9 Months Ended
	Jun. 30, 2014	Jun. 30, 2013
Cash flows used in operating activities:
Net loss	$ (15,590)	$ (16,313)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	1,541	1,877
Stock-based compensation	4,466	3,305
Change in fair value of compound embedded derivative liability	0	(803)
Gain on disposal of assets	(137)	(153)
Loss on extinguishment of debt, net	1,594	0
Amortization of debt issuance costs	143	203
Amortization of debt discounts	1,365	1,890
Accretion of debt premiums	(15)	(126)
Change in operating assets and liabilities:
Accounts receivable	(294)	(1,001)
Inventory	(545)	179
Prepaids and other assets	(724)	(841)
Accounts payable	57	2,639
Accrued expenses and other liabilities	(278)	553
Deferred revenue	815	1,888
Net cash used in operating activities	(7,602)	(6,703)
Cash flows used in investing activities:
Capital expenditures	(1,157)	(575)
Proceeds from sale of fixed assets	183	156
Payments under licensing agreements	(510)	(342)
Net cash used in investing activities	(1,484)	(761)
Cash flows provided by financing activities:
Proceeds from the exercise of stock options and issuance of shares under ESPP	1,023	866
Net proceeds from the sale of common stock	26,805	54,668
Repurchase of 2014 Debentures	(14,606)	0
Consent fee on amendment of credit agreement	(308)	0
Increase (Decrease) in Restricted Cash and Investments	(687)	0
Repurchase and retirement of restricted stock units for payroll taxes	(1,251)	(620)
Other	59	(6)
Net cash provided by financing activities	11,035	54,908
Net increase in cash	1,949	47,444
Cash at beginning of period	68,863	23,891
Cash at end of period	70,812	71,335
Cash paid (refunded) during the period for:
Interest	4,471	4,917
Income taxes	180	(1,094)
Non-cash investing and financing activities:
Equity offering costs incurred but not paid	200	207
Licensing agreement obligation incurred but not paid	156	0
Reclassification of compound embedded derivative liability to additional paid-in-capital	$ 0	$ 2,096