Overview:
#TODO: add overview figure
This ia a several step image analysis pipeline:
- Identidy nuclei in dataset (use either CellProfiler or StarDist).
- Extract RGB images of single nuclei (only using Hoechst and HCMV gB channels)
- Use a pre-trained convolutional neural network to clasify images.
- Sort images based on classification confiedence into folders for manual check of classification accuracy.
- Choose folders to include in the analysis, then collect line scans (150 pixel wide) across nucleus for all cells.
- Determine mean intensity and SEM over three biologically independent replicates. Vizualize data.
Getting started:
#TODO: Add description of setting up environment (or add a docker hub link).
Open the GenerateIDs_Drawlinescans file and follow the instructions there