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sandraoluoch / github-slideshow

A robot powered training repository :robot:
https://lab.github.com/githubtraining/introduction-to-github
MIT License
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Contact Sheet Generation #12

Open sandraoluoch opened 4 months ago

sandraoluoch commented 4 months ago

Developing a workflow that generates a contact sheet of all the denoised segmentations. Segmentations of 16 different structures using 6 different models.

Current Workflow "\allen\aics\assay-dev\users\Sandi\emt-project-leigh\for-suraj\denoise-contact-sheet-generation.ipynb"

Important Folders Raw Images = "\allen\aics\assay-dev\users\Sandi\emt-project-leigh\for-suraj\raw" Predicted Images = "\allen\aics\assay-dev\users\Sandi\emt-project-leigh\for-suraj\seg-pred" Otsu Thresholded Images = "\allen\aics\assay-dev\users\Sandi\emt-project-leigh\for-suraj\seg-pred-otsu"

sandraoluoch commented 4 months ago

Here is what the current contact sheet looks like. At present, it only contains segmentation results from 3 models: Actin, CAAX and DSP. The goal is to further improve the contact sheet so that it is: 1) Easier to read 2) Images are the same size 3) Improve the workflow so it is more efficient 4) Formatted better. Instead of doing a contact sheet per timepoint (T=0,5,10,15,20), create contact sheets per model. Each contact sheet will then contain segmentation results from all timepoints of each of the 16 structures.

contact_sheet.pdf

Image