Jon Newman
Ming-fai Fong
2011-04-26

ChR2-based excitation of smelly-I2643 using custum stimulator and neurorighter.

Purpose: This is the fourth serious protocol being run through neurorighter using my Single HP-LED stimulator. I will be testing a variety of stimulation frequecies and pulse widths under three conditions: pre-ttx, ttx, post-ttx. This will give an idea of the light induced artifact I'm dealing with as well as the recover time from TTX.

1. Light Excitation Protocols:

	freq = [1 5 10 20 40 80]; % Hz
	width = [50 100 500 1000]; % uS ( note I switched 50 for 5000 in this one)

   are cycled through in random order. 20 second applicaiton each, 20 seconds
   between each resulting in 24 protocols over 16 minutes.All aspects of each pulse       are recorded as digital signal with the following bits:
	- bo = on/off
	- b1 = type (0 in this case)
	- b2-8 = freq (Hz)
	- b9-22 = width (uS)
   
   Two protocols were performed per pharm. state:
	
	1. 2011-04-26_pulse-sweep-raw (~60 second long protocol with 5 pulses at each 	parameter combo, 1 second between. All raw streams were recorded. One instance 	with and one without SALPA in the recording path).
	2. 2011-04-26_pulse-sweep (standard protocol mentioned above).

2. Activity blockade

	1. 1 uM TTX

3. Recordings (* = performed)

	01. 2011-04-26_pulse-sweep_preTTX*
	02. 2011-04-26_pulse-sweep-raw_preTTX_woSALPA
	03. 2011-04-26_pulse-sweep-raw_preTTX_wSALPA
	04. 2011-04-26_pulse-sweep_TTX*
	05. 2011-04-26_pulse-sweep-raw_TTX_woSALPA
	06. 2011-04-26_pulse-sweep-raw_TTX_wSALPA
	07. 2011-04-26_TTX-recover-10min-00* (wash 1)
	08. 2011-04-26_TTX-recover-10min-01* (wash 2)
	09. 2011-04-26_TTX-recover-10min-02* (wash 3)
	10. 2011-04-26_pulse-sweep_postTTX*
	11. 2011-04-26_pulse-sweep-raw_postTTX_woSALPA
	12. 2011-04-26_pulse-sweep-raw_postTTX_wSALPA
	
NOTES:

- channel 31, 41, and 63 are no good and should be removed post-hoc
- 30 min spont recording taken before each protcol, and after wash
	- 30 min spont b4 protocol is incorporated into the protocol recording
- Application of drugs
	- Peform 3 full media changes using 1 uM TTX
- Washes
	- Peform 2 full media changes using jimbos
	- Record for 10 min
	- Examine file size, has it stabilized (NA on first recording)? If not, 		repeat.
- Spike detection
	- For pulse:
		- 5 RMS, 1000us dead-time, 80 uS min spike width, min slope of 3 uV/ms
		- fixed-RMS algorithm
	- For cont:
		- Noticed that adaptive may not be the way to go since FR is so high 		at points
		- used fixed. Should compare these two.
- SALPA
	- After doing recording 06 above, I realized that SALPA really reduces the 	light induced artifact. For the rest of the recordings, I used it. Thus, 04 can only really be compared to 10 and not 01.
- Temp
	- Retulated to 35 deg using Peltier