AIDA-3D preprocessing

Scripts for preparing data (Imaris format) for visualisation in AIDA-3D

Deployment:

1. Clone repository:

https://github.com/3DxN/Aida3Dpreprocessing

2. Create and activate a Python virtual environment (required Python version: ...):

Linux:

python -m venv venv
source venv/bin/activate

Windows:

python -m venv venv
venv/bin/Activate.ps

3. Install dependencies:

pip install -r requirements.txt 

Data processing

Steps include:

• Converting Imaris data to TIFF
• Generating HnE

1. Convert Imaris data Imaris data is assumed to include a metadata xml file describing the geometric arrangement of tiles and relative file paths to data of individual tiles. Tile image data is stored in .ims files referenced by the .xml file.

~/OMAL/250916aida3dData/012523_303_1_63X_stitchable.xml

python genHnE.py data/012523_303_1_63X_stitchable.xml --TIFFwriteout ./data/TIFFtiles 1 --nuclearChannel 3 --cytoChannel 4 --fixedZposition 11

2. Run segmentation

python src/segmentation/predCellpose3D.py --inDir data/TIFFtiles/ --outDir data/CellposeSegementations --tileJsonFilename data/features/tileArrangement.json

3. Run CD8/GH2AX analysis

python src/proximityAnalysis/analyze_multi.py 

Note: Set parameters in file src/proximityAnalysis/config.py (to be replaced by argparse interface)

4. Plot results

python src/proximityAnalysis/plotRatios.py 
usage: PlotRatios [-h] [-p PLOT_OUTPUT_FORMAT] [-c [CLASSLIST ...]] [--num_pseudo_classes NUM_PSEUDO_CLASSES]
                  pct_cd8_json_file pct_gh2ax_json_file mean_intensity_gh2ax_json_file
PlotRatios: error: the following arguments are required: pct_cd8_json_file, pct_gh2ax_json_file, mean_intensity_gh2ax_json_file

e.g.,

python src/proximityAnalysis/plotRatios.py pct_cd8_2026_02_19-11_24_40.json pct_gh2ax_2026_02_19-10_55_23.json mean_intensity_gh2ax_2026_02_19-11_24_40.json -c control control -p pdf