I have been using the WRMTRCK software for thrashing analysis of worms, however once changing to a higher resolution video the software is not recognising any of the worms and is coming up with ‘0 objects’ in the results section. Does anyone have any suggestions on what to do?
Hi @bs15jm and welcome to the forum!
I haven’t used wrmtrck myself extensively, but I’d assume the parameters
maxSize in the plugin dialog would need to be adapted to the new resolution.
I’ll also mention @jsp, the author of the plugin, here, in case he wants to give further advice.
BTW: @jsp, I noticed that the source code of the plugin is available, but no explicit license info is given. Would you be fine with licensing your code under a permissive license (such as LGPL, BSD or MIT) so that others can contribute improvements and re-distribute the code? Also, do you happen to have a version history (e.g. in form of a git repository), or are the previous versions linked from the plugin page the only available ones?
Thank you for your quick response. Sadly I have already tried altering the minimum and maximum pixel size (even going so far as 1,000,000) and even then it recognises the wrong number of objects and registers 0 movement at all.
I’ve read the pdf instructions extensively and have also watched the video tutorial and just can’t figure out why it isn’t working. I’ve removed flickering, set the threshold and subtracted the background and tried various values for min and max.
Are there any other parameters I may need to alter? And at 1600x1200 resolution do you know whether I also need to set a scale to help and what this would be?
I made wrMTrck a while ago now. wrMTrck uses the “Analyze” -> “Particles” function of ImageJ. So if you process and threshold your video so that Analyze Particles finds your animals, then so should wrMTrck.
That being said I don’t know if I ever tested 1600x1200 pixel videos.
If you clear the scale the output will be pixels. If you set the scaling you can get output in real distances (e.g. mm or µm)
If you continue to have problems with the analysis you could share the video so I can download it and give it a try.
I have been meaning to put the wrMTrck project on GitHub, but I haven’t had the time to figure out how github works.
I have started using Jupyter and GitHub at work so the learning curve and activation barrier may not be so step in the future.
Since I stole much of the code from MTrack2 https://valelab4.ucsf.edu/~nstuurman/IJplugins/MTrack2.html by Nico Stuurman - it should have the same copyright as the original version.
I am having problems in using wrmtrck for thrashing analysis. I follow youtube tutorial and if I use the same settings I get 0 objects, can be because my video has a different zoom? I tried to change the parameters and now I have the correct number of objects but still tracking is not working and also the final number of bends per object is not comparable to manual ones. anyone can help me pls? thank you