Export objects as masks for Fiji's ROI manager

Dear friends,

Is it possible to export the ilastik identified objects as ROI masks for use in Fiji’s ROI manager? Thanks!

Hi @bli,

welcome to the forum!!

The only way I know to translate from object classification is to use “analyse particles” in Fiji on the classification result. There is currently no way to directly export rois from ilastik.


Hi Dominik,

Thanks! That will be a good feature to have in the future release!

Best regards,

Hi @bli,

If your image is 2D and you export the object identities view then when you get in FIJI, if you have the update site for the SCF MPI CBG plugin installed, then you will have a command that can make that happen.
Find it at: SCF > Segmentation > LabelMap to ROIManager.

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Hi @lmurphy i think this is what I need! Thanks a lot!