Groups by channel metadata cannot be created

Hi everyone,

I’m trying to make a projection from a few z-stack pictures, and extraction of metadata by a channel category does not work when I try to group the images for the projection. The names are straightforward (eg. “Image_Z001_CH1.tif”), where the Z is a z-stack number and CH is channel number (1-4). I used this expression:

^Image_.*_CH(?P[0-4])

which results correctly in this:
Picture1

When I go to Groups to categorize by Channel, it only says nan.

When I try the same type of grouping with the Z-stack number instead, it works.

I’m using CP 4.0.7 Here’s the pipeline:

Grouping1.cpproj (836.8 KB)

Here are the pictures:

1_06.zip (4.3 MB)

The goal is to get a projection image for each of the 4 channels from all the pictures uploaded.

Also, in the end, the the output projection images are nowhere to be found. Can I continue my following pipeline dircetly after the projections, or do I have to first save the created pictures and then use them in another pipeline?

Thank you for any help.

Peter

Hi @Peter_Hamor,

In your NamesAndTypes module you match each image set based on channel. This means that a single set has multiple channel variables and so wouldn’t work as a group. Are you sure it’s channel you want to group by?

In other words, if in each set the blue image is channel 1, and the green is channel 2, it’s not possible to divide images into groups using ‘channel’ without breaking the image pairings. It seems more likely that you’d want to group by plate, or not at all. Each channel will be projected individually in your pipeline.