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Messages - Honi

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Surgery and Baseplating / Re: Rat
« on: January 24, 2019, 10:07:56 PM »
I didn't end up getting it working.  I might have if I was a better surgeon...

No, it does not.  The CNMF-E code is available on github. is the python version, and is the matlab version, which is extended here

Optics / Relation of scope slider direction and achromatic FL
« on: September 11, 2017, 09:31:33 PM »
What is the relationship between the direction that you would want to move the miniscope slider in, and the focal length of the achromatic lens?  I.e., if you are consistently wanting to move the slider so far that it falls out (too far up), would you want a larger or smaller focal length of your achromatic lens?

Electronics / Re: Question about group ordered PCB boards and sensors
« on: August 16, 2017, 09:10:15 PM »
No, I don't mind. 
Also, Jon Newman in Matt Wilson's lab has a panelized version that he got done at OSH park, you may want to contact him to get the link for that.

5 Suggestions / Re: Integration with Bonsai
« on: August 16, 2017, 12:26:57 AM »
Jon Newman has created a Bonsai plug-in for the miniscope.

Electronics / Re: Question about group ordered PCB boards and sensors
« on: August 16, 2017, 12:21:11 AM »
We had good experience ordering the LED PCBs from OSH park.   They are smaller than OSH park's minimum size, so you will have to cut the extra off with wire cutters or some such.

Electronics / Re: Coax communication frequency
« on: August 16, 2017, 12:12:25 AM »
We have found CRJ-05 to work fine for rats. It requires a bit of starting torque (~0.4N*cm), so may not work for mice. It is designed for high frequency coax communication though. The quote we received was ~$250.

Surgery and Baseplating / Re: Histology
« on: March 20, 2017, 06:21:17 PM »
The answer to this is no, it is not necessary to add any tags or do any immuno.  GCaMP-infected neurons fluoresce green on their own.  You would need to do DAPI at the same time to get the outline of brain structures to compare the GCaMP expression to.

Optics / Re: Longer GRIN lens
« on: March 02, 2017, 01:45:48 AM »
Sounds like a plan! I don't quite understand the mechanics though.  Is the glue adhesive between the lenses or between the lens and the tube?

Optics / Longer GRIN lens
« on: March 01, 2017, 11:18:14 PM »
We are trying to get the imaging working in rats.  One issue is that the 0.25 pitch lenses are too short.  Are there any ~2mm diameter relay lenses?  Are there 0.75 pitch GRIN lenses? 

System Assembly Troubleshooting / Re: Soldering SMA cable to DAQ PCB v2.3
« on: December 07, 2016, 07:40:23 PM »
If v3.2 doesn't need the SMA cable soldered to it, why are there still pads?  Should we just ignore them?

Data Analysis / Background analysis questions
« on: November 09, 2016, 07:46:10 PM »
I'm running the analysis toolbox on Animal G95/Day7/H19_M30_S21.  I have some background questions:

What are the units of ms.time?  It seems that it is taken from timestamp.dat.  What is the units of sysClock?

What is the difference between ms.trace and ms.originalTrace?

Thank you for your help.

Surgery and Baseplating / Histology
« on: November 03, 2016, 09:12:14 PM »
To assess efficacy of the virus, one would do histology a month after the injection.  Is there anything that needs to be added to the preparation such as an antibody or tag?  Or does the GCaMP just fluoresce on its own after fixation?

Surgery and Baseplating / Rat
« on: September 26, 2016, 04:02:46 PM »
Has there been any success with getting the imaging working in rats?  What virus do you use?  Any changes to the protocol?
Thank you

Electronics / Re: Coax communication frequency
« on: August 22, 2016, 12:41:04 AM »
Ok.  I found 50Ohm coax commutators that are cheaper than the dragonfly one and will let you know how it goes. 

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