Dear Ilastik developers,
We want to report a bug . We are using the modules 1) pixel classification routine, followed by 2) Boundary based segmentation with Multicut.
The bug creates extra superpixel areas/segmented regions, presumably derived from the bottom layers of the z-stack. However, these extra areas are maintained and shown in the upper parts of the stack (on the right side of the images), where there should be background - as the is no signal to create boundaries in these layers. Training with multicut to try to remove them does not solve the problem. Pls See screenshot of the output w/ incorrect regions circled in in red.
We have used Ilastik versions 1.3.2 and 1.3.3 and running them on a Mac (OS Mojave 10.14.4, w/ 16) and we’ve also reproduced the same bug in a Windows machine with the same data set- bug seems platform and version independent.
The following files might allow you reproduce the bug (pls click the link below to download them:
The file has:
- Input image confocal stack.
- Pixel classification project file - with trained data.
- Resulting annotated probability mask from pixel classification used as input for Boundary based segmentation w/ multicut
- The Boundary based segmentation w/ multicut project - with trained data set.
- The Boundary based segmentation w/ multicut output.
- A detailed description of what I am did procedure wise.
Please contact us back in case you think this can be fixed, or if you want additional input. We would love to use this platform for multiple projects going on at the lab now.