Cellprofiler analyst .nd2

Quick question, how can I load in .nd2 files into cellprofiler analyst and get a different channel than the first one?

Hi @mdl54,

I deal with ND2s a bit in CellProfiler so I know the trick.

Once you’ve dragged them into the Images module you need to go to the Metadata module and set a Metdata extraction method to “Extract from image file headers”. Then you need to click the “Update Metadata” button below and then the Update button on the table.

The order is important! If you click the update button first it won’t work and you have to clear the image and re-drag them in.

Once you’ve done that you should see the table fill up with data. Then the NamesAndTypes module you can set rules to be stuff like “Metadata | Does | Have C Matching” to give your different channels meaningful names to carry them forward to your analysis.

Hope that’s clear. Let me know how it goes!


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I got the metadata to update correctly, but I can’t filter using the namesandtypes module, it says theres a GC overlimit or something

Hmm, sounds like a memory limit. Do you have a lot of files with a lot of slices each?

Maybe try and increse the Java memory in the Preferences settings to see if it makes a difference (as long as you have more memory available on the computer you are using).