Metadata Reading Problem

Usage & Issues
#1

Hi There.

I think cell Profiler is struggling reading OIR (Olympus native format) metadata. The files are readable by the software, but the metadata is a problem.
I have try too the file as a Tiff and also It doesn’t work.

I think I need the information of the Metadata to be able to apply the (make projection) task and run the pipeline after that.

Please any comment ate suggestions are super welcome.

Thank you very much

Alfonso

#2

Hi @Raincoat

Would you be able to upload a sample image and the pipeline you’re using?

Thanks

#3

Hi David, for your time to help me with this.

Please find the image and pipeline using the LINK

Thank you very much

Alfonso

#4

Hi Alfonso,

Can confirm the oir file doesn’t open for me (we can look into that) in CellProfiler, but the TIF seems fine-

image
image1614×558 206 KB

There are a couple of issues in your pipeline-

A) Once you are splitting out all 40 planes x channels, you can no longer load them in as a color image to be split later, you need to load each frame individually in NamesAndTypes- such as this (do for all channels in each plane, to end up with an image set list that’s the number of channels you have wide, and the number of planes you have long):

image
image1540×462 74.3 KB

image
image918×492 112 KB

B) You can’t make a projection and use it in the same pipeline- CellProfiler can’t “loop through” all 10 planes, project them, and then run the rest of your pipeline on the projected image- you need to save out the projection, then load it into a new pipeline. The pipeline here will work to project your images.

Best of luck!

Projection.cppipe (8.6 KB)

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