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WayScience / Benchmarking_NF1_data

Benchmarking data processing strategies for Cell Painting data of NF1 Schwann cells. See analysis repository (https://github.com/WayScience/NF1_SchwannCell_data_analysis) for information on how the data was interpreted.

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Add images to 0_download_data #5

Closed jenna-tomkinson closed 2 years ago

jenna-tomkinson commented 2 years ago

@gwaybio I have added the files into a NF1_Images folder. This is ready for review.

jenna-tomkinson commented 2 years ago

@gwaybio

I know you said you don't have to review but can you confirm that the description of the data is fine? I am going to make a figure to describe the file metadata format like what CFReT did which is easy but I want to confirm the rest.
The relative paths in 1_preprocessing_data is not the same as this so I will make a PR to change those. I had the images within that folder so now that we have a module for it, no need for the raw images to be there!

I will have these corrections done by Friday!

gwaybio commented 2 years ago

Looks good. Can you add a couple more details? Ask yourself, "what do people need to know to understand what the data are". Details like:

Assay: Modified Cell Painting (what do the channels represent? What cell structures are they targeting?)
Cells: Schwann cells
Samples: (you have the detail about genotype already!)
Microscope: GE Deltavision Elite
Magnification: 20X (I think)
8 vs. 16 bit?
Anything else?
How many images?
etc...

jenna-tomkinson commented 2 years ago

@gwaybio Before I update the relative paths in the preprocessing module, I wanted to make sure this PR is completed first. It is ready for review!