Import several single planes as a multi-Z image

Image Analysis
#1

Hi all,

I am just starting using CellProfiler and have a very naive question.

I have a single folder containing numerous tif files. Each tif file contains a single plane.

But some of them belong to the same field, but are different Z positions. They are named something like
W1F001T0001Z01C1.tif
W1F001T0001Z02C1.tif
etc…

I would like to group them in some way so that the input sent on the analysis modules is the full Z-stack.
Then I would like for instance run a projection, etc…

I tried using the grouping tool, based on the z metadata extracted from filenames.
However, the analysis modules all parse each individual plane nonetheless.

How would you achieve this?

#2

Hi,

It sounds like you’re on the right track. There is a tutorial here which might help, called Loading Image Stacks and Movies: cellprofiler.org/tutorials.shtml

But the basic idea is to use the Metadata module to identify something unique about the planes as well as something that groups them, and then use the Groups module to group them. You could post a sample Z-stack (Dropbox or another service might be needed) plus your pipeline attempt and we can take a look. It’s not as easy to do as one might hope!

Hope that helps,
David

1 Like
#3

Thanks @David_Logan I will look into this in details.