WorMe

WorMe is a software for Caenorhabditis elegans length determination in microscopical images.

Developed by Josep Llobet, documentation helped by Nria Garriga, lead by Anna Laromaine, at Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC)

Group of Nanoparticles and Nanocomposites Institute of Material Science of Barcelona (ICMAB-CSIC)

Documentation

For detailed documentation please check out the user manual.

Citation

The software can be cited using the DOI provided by DIGITAL.CSIC: https://doi.org/10.20350/digitalCSIC/17417

Contributing, Reporting Issues and Support

For bug reports and feature requests, please open an issue on the GitHub issue tracker.

For code contributions, please fork the main branch, push your changes to your fork and create a pull request.

Please feel free to create an issue if you have any questions or comments. Developers can be contacted at alaromaine@icmab.es (Anna Laromaine).

Files

• LICENSE: license file, please read.

• /source/: Source code for the WorMe length determination software

• /documentation/: User Manual

• /paper/: Paper submitted to JOSS journal

• /examples/: Example images and results

Installation

WorMe is a MATLAB application for Windows. It does not require a MATLAB licence. The software binaries and source code are found here. - Install as local software from the executable or install file. In Windows. - Execute the source code, WM_length_determination.m, from the MATLAB Desktop environment software (version >2021b). Requires a MATLAB licence. In Windows, Linux or Mac. - Execute it as a runtime-dependent file after installing MATLAB Runtime (version 9.11). No license required. In Windows.

More details can be found in the Installation guide.

Fast Tutorial

There are five steps to use WorMe.

1. Image selection: Select the images to analyse. We will use this image as an example.
   

1. Scale setting: Set the measuring scale by selecting the scale bar. With "Select Automatically" the user must double click the scale bar and then input the displayed length number. In this example, it is 200.

2. Image processing: Configure the image modifications. Select from the Saved options in Processings the one that shows the worms the best. In this case, we used Modif_Example_4.txt. Then, press Analyse.

1. Worm selection: Select the worm objects manually. If the marked object is a worm, press the green checkmark. If it is not, the red cross. The Tools can modify the objects: the Scissors cut the current object in two, the New Object allows the user to trace a new object, and the Extend Object allows the user to lengthen the current object. Then, press Done.

1. Results: Press the export button to save the data. Select the "Export manual error corrected data" if the data requires comparison with other manual methods of measurement such as ImageJ.

For a detailed tutorial please check out the Use of the program section in the User Manual.

This project has been granted by the JAE Intro grant for the introduction of young people to the research, by the Ministerio de Ciencia, Innovacion y Universidades (ciencia.gob.es) y el Consejo Superior de Investigaciones Cientficas (CSIC).