search

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.
Creative Commons Zero v1.0 Universal
6 stars 18 forks source link

1 preprocessing data #2

Closed jenna-tomkinson closed 2 years ago

jenna-tomkinson commented 2 years ago

Added the three pipelines and edited them to have section titles (like the examples from Peng lab) so that someone can understand what is happening when looking at them.

jenna-tomkinson commented 2 years ago

@gwaybio

  1. I made three notebooks for organization reasons but technically one jupyter notebook that shows the steps and the next user adds their own images would be just fine. I think this is also in reference to the absolute versus relative paths and I will need to look into this since I am not sure how to write relative paths.
  2. I will use this code but I have been using Visual Studio Code over the terminal itself since it is much nicer to work with so I will work on this! I was wondering if I can gitignore the pipelines I created for each channel and just create a "new" one that is more generalized?
  3. As for the saving of the images as files, Roshan's code uses skimage.io.imsave and looking over the documentation on the GitHub, I saw no function or code for downloading the data post-correction for pybasic.
gwaybio commented 2 years ago

I was wondering if I can gitignore the pipelines I created for each channel and just create a "new" one that is more generalized?

you can use git to remove old files and add a new generalizable one - no need to add to gitignore (unless you want to keep the single channel notebooks, then yes, adding to gitignore will keep them locally, but remove them remotely).

skimage.io.imsave

Sounds good, I agree this is the way to go!