Multiplexed Protein Map analysis
This section explains step-by-step the image analysis protocol from the generation of cell segmentations in Cell Profiler 1 to the identification of Multiplexed Cell Units and finally to the creation of Multiplexed Protein Maps.
Protocol
Quick description of the 6 scripts:
|
Spatial projection of Multiplexed Cell Units on to a group of cellsMaterials needed:
CellProfiler1 cellatlas.org or cellatlas.org/downloads version 1.0.5811Bugfix Custom 4i modules cellatlas.org/downloads Scripts for generating Multiplexed Protein Maps cellatlas.org/downloads R and FlowSOM https://www.r-project.org/ https://bioconductor.org/packages/release/bioc/html/FlowSOM.html Phenograph and tSNE (cyt implementation) 1x computer (Ideally 1x high-performance cluster for the image analysis) Download
![]()
![]()
![]()
![]()
|