And I haven’t been able to run it to completion because I keep getting an error on step imagemath#22 that says error the image sizes don’t line up and to use the crop or align tools but I have followed the rest exactly and the align tool doesn’t work on 3D analysis. I’m at a dead end and not sure how to fix this, any help would be really really appreciated. Thanks.
You have two channels (in your attached sample images), but this pipeline is designed for a 3 channel image.
Please make sure in the “NamesAndTypes” module to adjust the channels and then moving forward ( in “RescaleIntensity”, “ImageMath”, etc.)
You can deactivate any module that you don’t need to use just by unchecking them.
Thank you so much this worked! I am now getting another error further downstream that states "error while processing overlay objects: ‘image’ and ‘label’ must be the same shape. I’m guessing the solution is something similar but I can’t figure out the size of the label. the input is rescaleintensityDNA, the output is nuclei overlay, the objects is Nuclei (from resize objects) as stated in the pipeline. Any ideas how to resolve this?
Thanks in advance!
I had this issue earlier, but I resolved after using the proper resizing factor as mentioned before in this thread. I tried your sample, reproduced the error but not able to resolve it. But found this thread,