CP 'save images' after 'make projection' not working

Hi I am attempting to flatten some Z stacks and save the resulting image for downstream analysis.

The save image module works (including the little green checkmark) when I try to save the source image, but when I change to the projection, the save module doesn’t work (and no little green checkmark).

If this uploads correctly, the script has one example for the two cases above.

Projection.cpproj (1.4 MB) Projection.cpproj

It is possible that CP doesn’t like the way I grouped the images to get groups of 4 z planes.

Thanks for any help/insights!

Steve

Hi Shaney314,

Your grouping looks fine. Its just that in the save images you chose “When to save as Last cycle” instead of Everycycle. Because I think you might want to save every channel MIP right?
When you chose “Last cycle” little green mark is back.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
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Hi Lakshmi,

Thank you very much for the suggestion. It did allow the pipeline to run, but it didn’t actually save any images. I think I have a problem with Names and Types, which separates the two channels for pairwise analysis, but when I group under ChannelNumber, it reports ’nan’.

I’m still working on it.

Cheers,

Steve

Hi shaney314,

I have edited your regular expression. I think it had a problem. Please find the attached pipeline with the edited regular expression. Try, it is works. Another option you can change in “NameAndTypes” as File contains “ch1” in your case instead of Metadata contains Channel…

Ensure that you choose the output folder is fine.
Projection.cpproj (209.4 KB)

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For Cellprofiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Join us at the High Content Analysis Symposium Oct 21-22, London
Society for Laboratory Automation and Screening

SLAS 2019 Advanced 3D Human Models and High-Content Analysis Symposium

Read more on our site.

Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging