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WayScience / pyroptosis_signature_image_profiling

This repository contains the pipelines used to analyze the data sets from the Interstellar collaboration.
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run cp analysis and extract single cells #3

Closed jenna-tomkinson closed 1 year ago

jenna-tomkinson commented 1 year ago

@gwaybio

I will make this into an issue, but I wanted to write it here first since part of this PR includes this.

I noticed that the "plate" names (which are the waves/parts of one plate) included spaces that created issues with pathing. For example:

One wave is named: 70117_20230118MM1_Ab Test_10X__2023-01-24T16_38_48-Measurement 1 It has spaces between Ab and Test and between Measurement and 1.

It is easy for me to get rid of the spaces, but if we had a lot of plates/waves, then this would need to be automated.

jenna-tomkinson commented 1 year ago

@d33bs

Could you please review my PR?

jenna-tomkinson commented 1 year ago

@d33bs

Can you please go over the commit 4c5cb2bed025b5f9b55dadd65d3f32869b04e85d and see if you have any improvements?

I will say the only downfall currently is that I do not have an environment specifically for the pe2loaddata software, it is just in base.

I will merge after your review.

jenna-tomkinson commented 1 year ago

@d33bs Thank you so much for the review! Merging it now.