Dealing with multichannel Z stacks in ilastik

Dear ilastik team,
This is actually a feature request. I’m using ilastik to segment multicolor Z stacks. I’m lacking some basic functionality to deal with different channels when placing labels. It would be great if there is an option to switch different channels on/off just for visual purposes. When dealing with multicolor images one signal is sometimes covering the other and it makes it very difficult to decide where to place the label. Also an “interactive” image histogram in some corner would go a long way in improving user experience when image needs to be made brighter or more “contrasty” for the purpose of deciding where to put the label. The current implementation of using the mouse “click and move system” to adjust contrast is very confusing and it only works with grayscale images.

Hi Vibor,

those are really great ideas! And yes, it’s absolutely true that working with multi-channel images could be way more convenient. What I usually do, is to set channel display to Grayscale. You can do so in the Input Data applet by double clicking the dataset. The dialog shown below will pop up and there you can change this display property.

you can then go through the channels one by one via the layerstack (the thing in the lower left corner):


Having a more finer grained control would be awesome though. Especially if you think further; one could include/exclude certain channels for classifier training and yet still use them to aid annotations.

Also the window/level (contrast) “feature” needs a little getting used to, I agree. For me it is very helpful to know that, whatever I do, I can always reset by pressing the right mouse button.

I’ll add this to the next team discussion and see whether we can put any enhancements on our development roadmap.