Data and Software

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

Data

• Accompanying dataset for: “IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues”, August 24, 2021, https://doi.org/10.5281/zenodo.5244551.
• Iterative Bleaching Extends multi-pleXity (IBEX) 2D and 3D Microscopy Data, March 23, 2021, https://doi.org/10.5281/zenodo.4632320.
• Iterative Bleaching Extends multi-pleXity (IBEX) imaging method, mouse spleen, December 3, 2020, https://doi.org/10.5281/zenodo.4304786.

Software

• 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).