Using extract (2021)

[omidm7]

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

[bahanonu]

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]

@omidm7 This is updated in the most recent version.

[omidm7]

Hooray! Thanks 🙏🏼 On Mar 26, 2021, at 07:50, Biafra Ahanonu ***@***.******@***.***>> wrote: @omidm7<https://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 GitHub<#68 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKRCGHBKSCVPREQWRZ3Z6QLTFSNMDANCNFSM4Z2OWBBQ>.

[omidm7]

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]

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]

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

[omidm7]

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

2021_04_08_p001_m01_NULL000_extractAnalysis.mat.zip

[bahanonu]

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