I’m using the “Tracking with Binary mask” workflow to track the objects in my images.
Here is what I’ve done:
- I got my workflow trained and saved.
- I have the segmentations of each of my raw data image (*_Simple Segmentation.h5)
Now I want to track all my objects with the headless model.
There is one issue here. The normal command line would be :
run_ilastik.sh --headless --project XXX \ --raw_data img1.h5 img2.h5 \ --segmentation_image mask1.h5 mask2.h5
But now the masks given by pixel classification with option “Simple Segmentation” have an empty space inside the file name…
And that makes for example the
mask1_Simple Segmentation.h5 two files in the headless mode.
the mask1_Simple, and the Segmentation.h5.
Of course it won’t find anything like those.