This repository includes the scripts used for analyzing TMA data generated by Martina Giacomini from University of Helsinki (research group of Ahmed Al-Samadi, PhD). This is a collaboration project between Dr Synnøve Magnussen, UiT, Norway and Dr Ahmed Al-Samadi, University of Helsinki, Finland.
For input, raw unstitched .rcpnl files generated from t-CyCif experiment were used. Illumination correction, stiching and alignment, and dearray was performed using BaSIC, ASHLAR and Coreograph, respectively, and it was performed using the MCMICRO pipeline. Segmentation of the dearrayed core tif files were performed using STARDIST, and the core of this script was collected from the pipeline generated by the Farkkilab .
It is still under progress, but feel free to contact [email protected] if you have any question or suggestion.