3D Cellprofiler output?

I use cellprofiler a lot but for 2D images. I am trying to develop these pipelines for the 3D images in our lab. I have a question for the output. For example, one image is quite large, 80 stacks. The output has 12 columns of data per image, so my question is how is it broken down? Can I take an average of these columns and denote this as the mean result of the whole stack?

Also, curious to know if there are any developments for the identify primary objects and other modules will become available for 3D.

Thanks!

Hi @amycaitriona,

I am not sure if your are mentioning about the image data (any object data like cells, nuclei) csv file that cellprofiler gives. In any of the case, every column corresponds to a parameter for example, Volume, Area, count etc…whereas every row corresponds to the data for example, in case image data file every row is a image data, in cells output file, each row data corresponds to each cell.
Ensure that you had checked “Yes” for “Process as 3D” option in Names and types and given the corresponding parameters. Also, ensure metadata is considered properly to take all the stacks from an image.
If yes, then you should receive the data for the complete stack i.e. every row corresponds to an object or an image
So, I don’t think you should average every column together (check the header of the column).
To help further, may you provide little more details with respect to your images.

Regards,
Lakshmi
www.wakoautomation.com

Hi Lakshmi,

Thank you for your reply! Could you explain further how to consider the metadata properly?

Thanks
Amy

Hi @amycaitriona,

Metadata of the every image is being saved in the image headers during image acquisition. This can be viewed in the Fiji/ImageJ, when you open the image go to Image>ShowInfo or use Bio-formats importer to open your image in Fiji. These you could use to check if your Metadata of the image.
If the Metadata is there already stored in the image header, then CellProfiler reads it automatically. If not, you can upload as the external file too (I have never tried).

Regards,
Lakshmi
www.wakoautomation.com