Documentation/Tutorial

[dlevenstein]

We should have a tutorial script that uses the sample structures and shows the user how to use the basic I/O functions (LFP/spikes/sessionInfo, etc), and run a basic analysis.

[brendonw1]

This could be a good thing for someone to do in a new lab as they get to know the system. If no one else does this before hand, then I can have people in my lab do this as they learn over the next few months. Obviously if someone does this first that's great.

On Sat, May 19, 2018 at 4:06 PM, Dan Levenstein notifications@github.com wrote:

We should have a tutorial script that uses the sample structures and shows the user how to load LFP, load spikes, use the basic I/O functions, and run a basic analysis.

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[dlevenstein]

Another related thing that needs to be done is a function description list. Can be updated/improved as we add more functions to the repo.

Just putting this here for later notice to self or others.

[brendonw1]

What approximate format should this take? Maybe example problems experiments where people are walked through the relevant code?

[DavidTingley]

uploaded to dev branch. @raswanson can upload her tutorial, I'll work on one for ratemapping

[dlevenstein]

We just discussed this a bit. Sounds like Rachel actually made a quick tutorial for Omid and a visiting postdoc a few months ago. We're going to make a "tutorials" folder and put it in there and then we can expand it.

The thinking at this point was having a few tutorials - one basic that includes things like how to load lfp, spikes, sessionInfo. And then a few specialized ones with things like lfp-spike analyses or detection or detecting place fields.

[DavidTingley]

We should also update the Wiki to reflect this folder and its contents

[dlevenstein]

Jinx

[DavidTingley]

@brendonw1 @evilrobotxoxo Do you guys have any students that might make for good alpha testers for tutorial scripts that we put together?

[brendonw1]

Yeah I think so... we may try some place cell/field analysis. I assume that's a good direction to go for a pretty complete and yet basic analysis type?

[DavidTingley]

@brendonw1 let me know if this works for you guys, it's a quick tutorial on ratemapping and PF detection.

https://github.com/buzsakilab/buzcode/blob/dev/tutorials/bz_tutorial_rateMapping.m

[brendonw1]

Hey thanks David, this looks great. Can I ask how you get the proper .behavior.mat for place? Do you use this?: https://github.com/buzsakilab/buzcode/blob/a12ded5f4a6bd538bbdb926ad7b901d4c13722c8/preprocessing/positionTracking/LEDTracking/bz_processConvertLED2Behav.m

On Thu, Jul 5, 2018 at 10:24 AM David Tingley notifications@github.com wrote:

@brendonw1 https://github.com/brendonw1 let me know if this works for you guys, it's a quick tutorial on ratemapping and PF detection.

https://github.com/buzsakilab/buzcode/blob/dev/tutorials/bz_tutorial_rateMapping.m

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[DavidTingley]

or this for optitrack systems, they should both produce that same *.behavior.mat file format (with additional Z and orientation data for optitrack)

https://github.com/buzsakilab/buzcode/blob/a12ded5f4a6bd538bbdb926ad7b901d4c13722c8/preprocessing/positionTracking/optitrack/bz_processConvertOptitrack2Behav.m

[evilrobotxoxo]

So everything here gets posted to Slack, but it doesn't work in the opposite direction, I guess. Anyway, yes, I will have a couple of students/technicians in the next few weeks who will need buzcode tutorials. In fact, I would appreciate a buzcode tutorial for myself, in terms of the standardized structs and etc.

[brendonw1]

Sadly I haven't spent the $13K for optitrack yet :) But good to know which code to use

Thanks David

On Thu, Jul 5, 2018 at 11:29 AM David Tingley notifications@github.com wrote:

or this for optitrack systems, they should both produce that same *.behavior.mat file format (with additional Z and orientation data for optitrack)

https://github.com/buzsakilab/buzcode/blob/a12ded5f4a6bd538bbdb926ad7b901d4c13722c8/preprocessing/positionTracking/optitrack/bz_processConvertOptitrack2Behav.m

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[DavidTingley]

@evilrobotxoxo I wouldn't mind using the slack channel more often but it hasn't really been adopted by many lab members here. @dlevenstein we could make another push for using it?

[brendonw1]

Prob w slack is it’s yet another place to check. I prefer one place - which for the moment predominantly email anyway On Sat, Jul 7, 2018 at 11:19 AM David Tingley notifications@github.com wrote:

@evilrobotxoxo https://github.com/evilrobotxoxo I wouldn't mind using the slack channel more often but it hasn't really been adopted by many lab members here. @dlevenstein https://github.com/dlevenstein we could make another push for using it?

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[evilrobotxoxo]

I don't have any strong preference for using slack over email or the github web page. I had just noticed for the first time that messages on slack don't get cross-posted to github, but the ones on github get cross-posted to slack.

Lucas L. Sjulson, MD, PhD Assistant Professor Department of Psychiatry and Behavioral Sciences Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine Rose F. Kennedy Center, Room 227 1410 Pelham Parkway South, Bronx, NY 10461 cell: 646-528-9672 http://sjulsonlab.org

On Sat, Jul 7, 2018 at 12:39 PM, Brendon Watson notifications@github.com wrote:

Prob w slack is it’s yet another place to check. I prefer one place - which for the moment predominantly email anyway On Sat, Jul 7, 2018 at 11:19 AM David Tingley notifications@github.com wrote:

@evilrobotxoxo https://github.com/evilrobotxoxo I wouldn't mind using the slack channel more often but it hasn't really been adopted by many lab members here. @dlevenstein https://github.com/dlevenstein we could make another push for using it?

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[brendonw1]

We're still a few weeks away from this... we're working on training on spike sorting and I think we have motion tracking working well, but not yet tried on a full-length video.

We'll loop back to this

On Thu, Jul 5, 2018 at 11:29 AM David Tingley notifications@github.com wrote:

or this for optitrack systems, they should both produce that same *.behavior.mat file format (with additional Z and orientation data for optitrack)

https://github.com/buzsakilab/buzcode/blob/a12ded5f4a6bd538bbdb926ad7b901d4c13722c8/preprocessing/positionTracking/optitrack/bz_processConvertOptitrack2Behav.m

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[AntonioFR8]

I have started writing some documentation in the form of Contents scripts for each main folder. I will be uploading them this week. If anybody have strong opinion against I will also reorganize a bit the folders. Like creating a SharpWaveRipple folder inside LFP analysis were to put together related staff that is disperse now (i.e. in detectors)

[evilrobotxoxo]

I had my rotation student Andrea (not Andrea Cumpelik) try the buzcode tutorials, and she was (understandably) unable to figure out that she was supposed to run "compilefma" and "mex CCGHeart" first. Is there a reason we don't have compiled mex files in buzcode?

Luke

Lucas L. Sjulson, MD, PhD Assistant Professor Department of Psychiatry and Behavioral Sciences Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine Rose F. Kennedy Center, Room 227 1410 Pelham Parkway South, Bronx, NY 10461 cell: 646-528-9672 http://sjulsonlab.org

On Mon, Jul 23, 2018 at 12:13 AM, AntonioFR notifications@github.com wrote:

I have started writing some documentation in the form of Contents scripts for each main folder. I will be uploading them this week. If anybody have strong opinion against I will also reorganize a bit the folders. Like creating a SharpWaveRipple folder inside LFP analysis were to put together related staff that is disperse now (i.e. in detectors)

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[dlevenstein]

There's a function 'compileBuzcode' in the top folder. I thought we'd put in the readme that the user should run this before doing anything....... apparently we did not! I'll add it.

[dlevenstein]

(also, to my knowledge these files have to be compiled on the users computer)

[dlevenstein]

I just made some updates to the readme, that indicate the need to compileBuzcode first. Feel free to make it more helpful as you see fit!

[evilrobotxoxo]

Thanks, Dan!

Lucas L. Sjulson, MD, PhD Assistant Professor Department of Psychiatry and Behavioral Sciences Dominick P. Purpura Department of Neuroscience Albert Einstein College of Medicine Rose F. Kennedy Center, Room 227 1410 Pelham Parkway South, Bronx, NY 10461 cell: 646-528-9672 http://sjulsonlab.org

On Mon, Jul 23, 2018 at 2:34 PM, Dan Levenstein notifications@github.com wrote:

I just made some updates to the readme https://github.com/buzsakilab/buzcode/blob/master/readme.txt, that indicate the need to compileBuzcode first. Feel free to make it more helpful as you see fit!

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[DavidTingley]

As you have people go through it @brendonw1 @evilrobotxoxo let us know what other tutorials would be most useful to upload first.

[brendonw1]

Yes ... having issues earlier than all that now... but soon... I hope

On Mon, Jul 30, 2018 at 11:37 AM David Tingley notifications@github.com wrote:

As you have people go through it @brendonw1 https://github.com/brendonw1 @evilrobotxoxo https://github.com/evilrobotxoxo let us know what other tutorials would be most useful to upload first.

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[dlevenstein]

Add Thomas to this