Opening .ome.tif


We have some trouble using Cellprofiler2 with OME.TIF files.

It seems that CP is trying to open all the images that are specified in the OME.TIF header of one image file.
we attached the first image of such a data set.

(i) would it be possible to tell CP to open only the one actual image in the file that is loaded?

(ii) if CP opens all the associated images,
(iia) does it actually know how to handle them within the Image Analysis Pipeline??
(iib) does it apply the current pipeline to all the associated images in the OME set?
(iic) is there some option to work on a specific slice of the data set or to loop through it or something like this?

we suspect that the trouble comes from the fact that CP is using Bioformats for opening ome.tif files.
what about giving an option to use PIL instead?

All the Best,

Hi Tischi,

Could you post an example OME.TIF so we could take a look? At that point, hopefully, we can better answer your questions :smiley: