Welcome to ChromCon, the Chromatin Condensation Quantitative Analysis Project of the McCusker Lab

In this repository you can find the code corresponding to our publication Sosnik, J., Vieira, W. A., Webster, K. A., Siegfried, K. R. and McCusker, C. D. (2017). A New and Improved Algorithm for the Quantification of Chromatin Condensation from Microscopic Data Shows Decreased Chromatin Condensation in Regenerating Axolotl Limb Cells. PLoS ONE12(10): e0185292. We hope that you make use of our tools for your research. If you do, please cite our paper.

All the files are provided under the BSD 3-Clause License. You can access the terms on the license here.

There are two tools that we have made available here. The first one, Crop&Split is an ImageJ macro that allows you to mark an area in your z-stack and creates a new image with only the region selected in a loss-less fashion. Instructions about download, installation and how to use the tool can be found in the Crop&Split_Instructions file. This tool makes it easy to split your image stacks into folders with individual z planes that you can use as a starting point for the ChromCond tool.

The Second tool is called ChromCond and is the tool that performs quantitative analysis of chromatin condensation. This is a MATLAB tool but we have also provided a compiled version that you can download a use freely, even if you don’t have a MATLAB license. Instructions about download, installation and how to use the different versions of the tool can be found in the ChromCond_Instructions file.