Skip to content

Reworked complete pipeline and interface

Marco Dalla Vecchiarequested to merge
interface-project-rework into main

Update workflow for this project to be entirely performed through Marimo interface:

  1. Metadata table allows users to specify variables to create project folder structure
  2. Fiji is called through Marimo to create structure and process raw images
  3. QuPath projects and analysis is done through Marimo (as before), some steps are now in parallel to make it faster
  4. Measurements tables are now exported for every variable condition grouping
  5. User can now specify channel names to use in the exported figures
  6. An additional figure displaying the positivity cell area fraction on barplot with animal averages dots is also exported

Merge request reports