MISA++: A modular and high-performance framework for image analysis

Ruman Gerst (1,2), Anna Medyukhina (1), Marc Thilo Figge(1,2,*)

(1) Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany

(2) Faculty of Biological Sciences, Friedrich-Schiller-University Jena, Germany

* To whom correspondence should be addressed.

https://applied-systems-biology.github.io/misa-framework/

About

Segments cells with a distance transform watershed method.

Example data: https://github.com/applied-systems-biology/misa-framework/releases/download/1.0.0/misaxx_segment_cells_example_data.zip

Copyright

Copyright by Ruman Gerst

Research Group Applied Systems Biology - Head: Prof. Dr. Marc Thilo Figge

https://www.leibniz-hki.de/en/applied-systems-biology.html

HKI-Center for Systems Biology of Infection

Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Insitute (HKI)

Adolf-Reichwein-Straße 23, 07745 Jena, Germany

The project code is licensed under BSD 2-Clause. See the LICENSE file provided with the code for the full license.

Building

This project requires Maven (http://maven.apache.org/) and Java 8. Java 9 or higher does not work. If you need Java version 8, you can find it here: https://adoptopenjdk.net/

Run following command in a terminal:

mvn compile
mvn package

The compiled binaries will be placed in the target directory.

Usage

The program has following parameters:

• --input the input directory
• --output the output directory
• --threads <number> number of threads

The input directory must have following structure:

<input-directory>/<sample>/<experiment>/channel1.tif

There can be as many samples and experiments as required.