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bahanonu / ciatah

CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: https://git.io/ciatah_docs. Formerly known as calciumImagingAnalysis (ciapkg).
https://git.io/ciatah_docs
MIT License
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Using extract (2021) #68

Open omidm7 opened 3 years ago

omidm7 commented 3 years ago

Hi Biafra, Super excited that the new cell extraction method is released and supported by CIAtah! I was able to load EXTRACT into the external_programs folder, but under Cell Extraction Methods in the GUI, the only "EXTRACT" is still the 2017 version. Is this the correct method? Omid

image

bahanonu commented 3 years ago

Hey Omid, hope all is well. Yep, that is the correct EXTRACT method. I have that updated locally but need to push and merge the updated branch sometime today/tomorrow. Let me know if you encounter an issues while running EXTRACT.

cheers! -Biafra

bahanonu commented 3 years ago

@omidm7 This is updated in the most recent version.

omidm7 commented 3 years ago

Hooray! Thanks 🙏🏼

On Mar 26, 2021, at 07:50, Biafra Ahanonu @.**@.>> wrote:

@omidm7https://github.com/omidm7 This is updated in the most recent version.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/bahanonu/calciumImagingAnalysis/issues/68#issuecomment-808279375, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AKRCGHBKSCVPREQWRZ3Z6QLTFSNMDANCNFSM4Z2OWBBQ.

omidm7 commented 3 years ago

Hi Biafra. I've been successfully running EXTRACT on my laptop, but on the lab computer, I keep getting the attached error. post_extract_error.pdf

Could this be an issue of using Matlab2017b (desktop) vs 2020b (laptop)?

Omid

bahanonu commented 3 years ago

hey Omid, looks like the graphconncomp function is causing the error, does your 2017b installation have the Bioinformatics Toolbox installed?

Can you send the output of ciapkg.io.dependencyCheck on the MATLAB command line (no semicolon)?

omidm7 commented 3 years ago

Thanks, the 2017 version was missing Bioinformatics and a few other toolboxes. Updating everything now, should be good. Thanks again! O

omidm7 commented 3 years ago

Hi Biafra, Any idea what could be causing this strange partitioning problem? I experienced it with two separate data sets - for some reason the 4 quadrants are not merging smoothly. I've uploaded the configuration/user config files if it helps. Appreciate your help with this! Best, Omid

image image image 2021_04_08_p001_m01_NULL000_extractAnalysis.mat.zip

bahanonu commented 3 years ago

hey @omidm7, let me take a look at this and get back with any thoughts on what parameters could be tweaked.