This page lists publicly available datasets acquired using the IBEX imaging protocol and software that was specifically developed for processing and analyzing multiplex imaging.



  • SITK-IBEX: SimpleITK based software for aligning/registering images acquired with the IBEX microscopy imaging technique (GitHub repository, Python, License: Apache-2.0 ).
  • SimpleITK imaris extensions: SimpleITK based extensions for the imaris (Oxford Instruments) microscopy image analysis program. A variety of utilities including registration, channel arithmetic, virtual H&E staining and more. Extension programs can be run as standalone software without the need for the imaris software (GitHub repository, Python, License: Apache-2.0 ).
  • CytoMAP: comprehensive platform for spatial analysis of tissues, allowing researchers to explore complex datasets structured as a csv files, with at least x-y positional data (GitLab repository, MATLAB, License: MIT).