JRCLUST export

[WeissShahaf]

I tried to follow your instruction: Export to JRCLUST for manual curation. You need to clone JRCLUST and set the path path_jrclust in user.cfg. irc2 export-jrclust [path_to_prm_file]

-I could not find user.cfg anywhere, but i changed the JRCLUST path in default.cfg.

-Apparently the probe file it's looking for is a CSV, but none is created if using a .bin file. but even when supplying a CSV, i get multiple fail to copy messages

Copy failed: E:\ironclust\matlab\jrclust_patch//export_jrclust.m to ....\JRCLUST+jrclust+import\irc.m Copy failed: E:\ironclust\matlab\jrclust_patch//neCell2mat.m to ....\JRCLUST+jrclust+utils\neCell2mat.m Copy failed: E:\ironclust\matlab\jrclust_patch//processArgs.m to ....\JRCLUST\@JRC\processArgs.m Copy failed: E:\ironclust\matlab\jrclust_patch//loadProbe.m to ....\JRCLUST+jrclust\@Config\private\loadProbe.m

can you try to take a look at an example of our data and see if you can get it to run in irc2? and exported to jrclust?

https://www.dropbox.com/preview/test/test/GL383_20190822_OF_ExtraWall_g0_t0.imec0.ap.bin?role=personal

https://www.dropbox.com/preview/test/test/GL383_20190822_OF_ExtraWall_g0_t0.imec0.ap.meta?role=personal

[jamesjun]

Thanks. I only tested it on our .mda format but I should tests it on SpikeGLX format. IronClust GUI should be done this week.

-James

On Feb 13, 2020, at 7:45 AM, WeissShahaf notifications@github.com wrote:

 I tried to follow your instruction: Export to JRCLUST for manual curation. You need to clone JRCLUST and set the path path_jrclust in user.cfg. irc2 export-jrclust [path_to_prm_file]

-I could not find user.cfg anywhere, but i changed the JRCLUST path in default.cfg.

-Apparently the probe file it's looking for is a CSV, but none is created if using a .bin file. but even when supplying a CSV, i get multiple fail to copy messages

Copy failed: E:\ironclust\matlab\jrclust_patch//export_jrclust.m to ....\JRCLUST+jrclust+import\irc.m Copy failed: E:\ironclust\matlab\jrclust_patch//neCell2mat.m to ....\JRCLUST+jrclust+utils\neCell2mat.m Copy failed: E:\ironclust\matlab\jrclust_patch//processArgs.m to ....\JRCLUST@JRC\processArgs.m Copy failed: E:\ironclust\matlab\jrclust_patch//loadProbe.m to ....\JRCLUST+jrclust@Config\private\loadProbe.m

can you try to take a look at an example of our data and see if you can get it to run in irc2? and exported to jrclust?

https://www.dropbox.com/preview/test/test/GL383_20190822_OF_ExtraWall_g0_t0.imec0.ap.bin?role=personal

https://www.dropbox.com/preview/test/test/GL383_20190822_OF_ExtraWall_g0_t0.imec0.ap.meta?role=personal

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[WeissShahaf]

one more thing, for the imec3_opt3.prb that is the default now for neuropixels probes is not right. i guess it fits the phase3a probes.

but the commercial P3B2 / 1.0 probes are different. with only 3 reference sites.

i'm attaching the file i'm using, given to me by Jennifer Colonell over at spikeGLX imec3b_staggered.zip

[jamesjun]

Wonderful, thanks for sharing the latest mapping file. I will add it to the probe file library.

-James

On Thu, Feb 13, 2020 at 12:22 PM WeissShahaf notifications@github.com wrote:

one more thing, for the imec3_opt3.prb that is the default now for neuropixels probes is not right. i guess it fits the phase3a probes.

but the commercial P3B2 / 1.0 probes are different. with only 3 reference sites.

i'm attaching the file i'm using, given to me by Jennifer Colonell over at spikeGLX imec3b_staggered.zip https://github.com/flatironinstitute/ironclust/files/4199848/imec3b_staggered.zip

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[jamesjun]

I cannot download your files on Dropbox. Could you please create a sharable link and send it to me?

[jamesjun]

Dear Weiss, I have some questions about the probe file you made (imec3b_staggered.zip). There are three internal references and I expected you to exclude three sites but you excluded only one.

The phase 3A probe had 12 internal references and these channels do not contain neural recordings. Does probe 3B2 contain any useful recordings if the sites are not selected as internal references? The meta file you shared with me suggests that they were connected to external references.

[WeissShahaf]

i sent a new link by email.

On Fri, Feb 14, 2020 at 9:54 PM James Jun notifications@github.com wrote:

I cannot download your files on Dropbox. Could you please create a sharable link and send it to me?

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Shahaf Weiss, PhD Max Planck Institute for Brain Research NSK - Laurent department, room 1.120 Max-von-Laue-Straße. 4 60438 Frankfurt am Main, Germany www.brain.mpg.de https://email.gwdg.de/owa/redir.aspx?C=7VzwRsdzDhtbiu7Ahx29IRVoe1iNWVvSOlu_TVQfe5hwnyOM8RrVCA..&URL=http%3a%2f%2fwww.brain.mpg.de

(work) shahaf.weiss@brain.mpg.de (personal) shahaf.me@gmail.com Tel:+49 17657814689

[WeissShahaf]

there are 3 ref sites, i think one in each site bank. plus the tip reference. they cannot be used for recording.

i'm not sure why but the internal sites work in about 50% of the probes, and are noisy in others.

alternatively, you can use an external reference wire, which we use for both ground and ref when possible, for a good LFP signal. however internal sites, especially the tip site are good for removing movement artifacts in-vivo.

On Fri, Feb 14, 2020 at 11:23 PM James Jun notifications@github.com wrote:

Dear Weiss, I have some questions about the probe file you made (imec3b_staggered.zip). There are three internal references and I expected you to exclude three sites but you excluded only one.

The phase 3A probe had 12 internal references and these channels do not contain neural recordings. Does probe 3B2 contain any useful recordings if the sites are not selected as internal references? The meta file you shared with me suggests that they were connected to external references.

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Shahaf Weiss, PhD Max Planck Institute for Brain Research NSK - Laurent department, room 1.120 Max-von-Laue-Straße. 4 60438 Frankfurt am Main, Germany www.brain.mpg.de https://email.gwdg.de/owa/redir.aspx?C=7VzwRsdzDhtbiu7Ahx29IRVoe1iNWVvSOlu_TVQfe5hwnyOM8RrVCA..&URL=http%3a%2f%2fwww.brain.mpg.de

(work) shahaf.weiss@brain.mpg.de (personal) shahaf.me@gmail.com Tel:+49 17657814689

[jamesjun]

Thanks for letting me know. I added the bottom reference site back to the exclusion list.

-James

On Feb 18, 2020, at 4:12 AM, WeissShahaf notifications@github.com wrote:

 quick note: I see in the last commit you removed the ref site 192, from the imec3B2.prb, it is actually removed for the default setting (bottom 384 channels) because it cannot be used for recording. same for sites 576, 960 if using other channel configurations that are within that site range

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[jamesjun]

I still haven't tested JRCLUST export tool on your dataset but will get to it this week.