Extracting 3D measurements in CellProfiler 3.0

Hello,

I am starting to use CellProfiler with an aim to segment organoids in 3D and extract statistics. I have read a lot of tutorials but I cannot find a way to export the measurements of 3D objects since the export modules are not supported for 3D…

How can you export these 3D measures? I am intersted in cell shape and intenisty values.

Cheers

Hi @Rios_Lab,

Did you try using the export modules in your pipeline? They should work fine, it looks like the module help dialog just needs to be updated. If you’re still having trouble, could you confirm whether this is with ExportToSpreadsheet or ExportToDatabase?

Hope that helps

Hi DStirling,

Thanks for the reply. I will try it then. But I now run into another problem:
my 3D dataset is not recognized… I has an issue with the dimensions, although I did put the pixel size that I see in Fiji.
It does work fine if I process it in 2D though…
Do you have any advise on that?

Thanks!

Hi @Rios_Lab,

Would you be able to post the actual error you’re seeing? You may also want to check out the 3D tutorial we have here.

Hi David,

This is the error I get:

It start when I try to run the first module of my pipline.

I did read the tutorial indeed and also looked for some other related questions in the forum (CellProfiler Invalid Image Dimensions ), but still can manage it to work. I think it has something to do with the voxel size of the images. But I did check in Fiji the image properties…

Thanks!

Maria

Hi Maria,

Thanks for sending that, hopefully this will be a simple configuration issue. Would you be able to send a copy of the pipeline you’re currently trying to use?

Sure! In this link you can find the pipline. I also send you a small subset from my dataset.
Test dataset.zip (13.3 MB)
Thanks!

Maria

Hi @Rios_Lab,

I see the problem: 3D mode is designed to be used with image files which have planes in a stack within the same file, rather than a separate image file per plane. This is why it’s complaining about dimensions. If you don’t have tif stacks you could potentially convert your images using ImageJ or a separate CellProfiler pipeline with the SaveImages module in ‘movie’ mode.

Hope that helps

Ok great! I will try that. Thanks!

Hi David,

Thanks for the help. I manage to finish the pipeline. Now coming to my initial question. I can extract 3D features, but these are basically just volume and area of the segments. Is that normal. Are there no other 3D segment measures available?

Hi @Rios_Lab,

To capture additional features you’ll need to add additional measurement modules. There are numerous measurement modules to use depending on what you’re interested in. MeasureObjectSizeShape and MeasureObjectIntensity sound relevant and both support 3D objects, but you’ll need to run them before the export module in order to save the data.