Code accompanying our manuscript
"Spatial Correlation of the Extracellular Matrix to Immune Cell Phenotypes in the Tumor Boundary of Clear Cell Renal Cell Carcinoma Revealed by Cyclic Immunohistochemistry"
After aquiring all digital images, create new QuPath project and load the images using this naming convention CycleNumber_Marker_BlockID. Using the TMA dearrayer tool in QuPath select and remove cores that you want or dont want to analyze. Run the CoreExtraction.groovy script. This will create a folder called TMA_Cores in the QuPath project directory and each folder in it will have the extracted cores.
Open Fiji and run the script Deconvolution_Grayscale.py. The script will prompt to select the main folder where the extracted cores are. After selection, the script will automatically create a folder called "Processed_Cores" where all 2-channel images will be found.
Then setting the path to the "Processed_Cores" folder in the valis_registration_merge.py and selecting a new path for the merged cores (see comment) this script will register and fuse the markers of each core. For installing VALIS refer to the original documentation https://valis.readthedocs.io/en/latest/. Examplified Folder Structure is shown in Supplementary Figure S1
Special thanks to Chandler Gatenbee!