Animal Tracking workflow

example_tif-1.tif (2.8 MB) ### Sample image and/or macro code

Background

Hi all, I was wondering if anyone could help me with my workflow, still new to imaging data/analysis so sorry for any stupid questions. So far I’ve managed to get the animal tracking workflow to work quite well at tracking worms, but I’m now struggling to use this data. My end aim is to track the location of each worm and use this to split the original image into separate stacks per object, then straightening the worms for analysis.

Challenges

So far I’ve attempted generating/copying ROI generated in Fiji to the original image, however this doesn’t work as it only uses the ROI from the first/selected image of the timelapse. I could possibly convert my tracked image and original image into separate tifs for each frame and link each of them using a for loop, but this would still lack the labelling between frames.

I’ve looked into trying to re-track/label the tracking data using the wrmtrck plugin but this is unable to detect the objects in my already tracked file. Morpholibj is able to label my data but couldn’t work out how to access and use these labels to generate a ROI linked to each object that i could link to my original image.

Many thanks,

Jack