Call for tutorials

Looking for ways to analyze your dataset? Need help with a software package?
Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
Post Reply
Posts: 1
Joined: Sun Jun 21, 2020 6:52 pm

Call for tutorials

Post by juan.ojeda » Sun Jun 21, 2020 8:11 pm


I have been using the CellProfiler - Ilastik pipeline for the analysis of imaging mass cytometry for over a year. Although this pipeline is not easy to set up due to the many pieces of software to install and fine-tune (Anaconda, MCD viewer, imcSegmentationPipeline, imcPlugginsCP, CellProfiler, Ilastik and HistoCAT or IMACytE) it was very helpful a step by step tutorial that guided me through most of the analysis. I have seen that this is not the only pipeline, there are other interesting options and I would like to try them and compare results. I have tried to use ImageJ, ICY and QuPath and although they are easy to install, I haven't found any specific tutorials for imaging mass cytometry data analysis and I haven't managed to get results with them.

I would appreciate any guidance or tutorial on how to set up an imc data analysis pipeline using ImageJ, ICY or QuPath.

Post Reply