hansenjn/motiq

A set of ImageJ plugins to quantify dynamics, morphology, and fluorescence of microglial cells.

A set of ImageJ plugins to quantify dynamics, morphology, and fluorescence of microglial (or other) cells.

Included tools

• MotiQ_Cropper: An ImageJ plugin to efficiently select individual cells from single images, time-lapse images, static 3D images, or time-lapse 3D images.
• MotiQ_Thresholder: An ImageJ plugin to segment images for later quantification by MotiQ 2D Analyzer or MotiQ 3D Analyzer.
• MotiQ_2D_Analyzer: An ImageJ plugin to quantify the output images from MotiQ Thresholder in 2D.
• MotiQ_3D_Analyzer: An ImageJ plugin to quantify the output images from MotiQ Thresholder in 3D.

How to cite?

When using any of the MotiQ plugins, please cite MotiQ by referencing the MotiQ publication:

Jan N. Hansen, Matthias Brückner, Marie J. Pietrowski, Jan F. Jikeli, Monika Plescher, Hannes Beckert, Mareike Schnaars, Lorenz Fülle, Katharina Reitmeier, Thomas Langmann, Irmgard Förster, Delphine Boche, Gabor C. Petzold, and Annett Halle. MotiQ: an open-source toolbox to quantify the cell motility and morphology of microglia. Molecular biology of the cell, 33:11 (2022). https://doi.org/10.1091/mbc.E21-11-0585

Copyright notice and contacts

Copyright (C) 2014-2024: Jan N. Hansen.

Contact: jan.hansen (at) uni-bonn.de

How to use MotiQ?

Installing MotiQ

MotiQ is a set of ImageJ plugins that can be run in ImageJ or the extended ImageJ version FIJI. Please follow our installation guide in the MotiQ wiki to install FIJI / ImageJ and MotiQ to your computer.

Applying MotiQ

A manual is available here. Example settings can also be found in the original MotiQ publication. Note that MotiQ settings may require to be optimized for your data set before MotiQ can deliver perfect results. Visit the MotiQ wiki for more advice and information on optimizing and troubleshooting.

Questions? Ideas? Missing functions? Issues? Bugs? Unclear explanations in the User Guide?

Are you missing a function or a parameter in MotiQ? Is an explanation missing in the User Guide? Are you encountering problems with MotiQ?

If you can't find an answer or solution in the MotiQ wiki or User Guide, please let me know and report your issue either by submitting it to the issue tracking systems in github (please note that this will be publicly visible) or by sending me a private message to jan.hansen (at) uni-bonn.de.

motiq's Issues

3D analysis terribly slow

The 3D analysis of a Z-stack took over three hours! Is this typical? I have a Windows 11 laptop with 64GB RAM and a 16 GB GPU.

On a different computer, I'm getting the following error message when I try to run MotiQ Cropper:

`(Fiji Is Just) ImageJ 2.9.0/1.54a16; Java 1.8.0_322 [64-bit]; Windows 10 10.0; 539MB of 48948MB (1%)

java.lang.NullPointerException
at motiQ_cr.Cropper_.run(Cropper_.java:110)
at ij.IJ.runUserPlugIn(IJ.java:239)
at ij.IJ.runPlugIn(IJ.java:205)
at ij.Executer.runCommand(Executer.java:152)
at ij.Executer.run(Executer.java:70)
at java.lang.Thread.run(Thread.java:750)

`
I'm not sure how to interpret this error message. Can someone please tell me what is wrong and how do I rectify it? Thank you very much.
Mary

Cell body / Cell soma parameters

It would be good to add parameters that quantify the cell body / soma of the cell (e.g., soma volume (3D) / area (2D)).

Calling MotiQ plugins from a macro

Issue / Request submitted from a user by email:
I would like to be able to run the 3D analyser part of MotiQ from the command line, I was wondering if there is any way to do this? Can I make it into a Fiji macro which I can then somehow run on a linux workstation without opening the GUI? I tried to record a macro but the command only opens the first dialog box, I couldn’t figure out how to make the code to automatically choose the files to be batch processed and to start the processing.

Thank you very much in advance for your help!