Classify pixels of a 16-bit image in ilastik 0.5

Hi CP Team,

I’m trying to work with 16-bit image from Cytation 5 in ilastik 0.5, and then export classifier to CP. The image can not be displayed properly in ilastik however. David showed me a workaround, but I forgot how to do it. It seems that ilastik open it as 8-bit image, and classifier is based on 0-255 pixel intensity, while CP open it as floating numbers, the classifier doesn’t work when it’s called in CellProfiler.

I’m also interested in learning new pixel classification function in CellProfiler. It will be great if anyone can point me to that direction. Thank you!

Unum Therapeutics

You should be able to rescale your images to 0-255 using RescaleIntensity’s “Convert to 8 bit” feature.

The new pixel classification feature can currently only be accessed by installing from source (instructions for different OS’es are on the right of this page) and then checking out that branch from GitHub- the name of the branch and some basic info about how it works are here.

Hi Beth,

Thank you so much! I will check it out. -Tianxiao