Image Analysis Toolboxes

Currently in biology, image analysis typically requires researchers to identify cells by hand or to use software packages that provide only rudimentary image processing capabilities and constraining analysis to certain cell types. This leads to time-consuming processes to analyze images, as well as the possibility of introducing researcher bias. To solve these problems, I am developing customized pipelines to automate the analysis of large imaging datasets.

The toolboxes listed below are open-source and are available for use by other researchers. The links below will take you to their Git repositories. Please have a look at the respective wiki pages for instructions on how to install and use these toolboxes.

MATLAB toolboxes

Python toolboxes


In addition to toolboxes, I have also written code to solve specific imaging issues.