Load 3D image from czi

Hi,

I was wondering if I could get some advice on how to upload files for 3D analysis. My images were originally in czi format, which I got to know is not supported for 3D processing in CellProfiler 3, so I exported them as tiff files. I have 4 channels and varying amount of z-stacks for each image which ended up being exported as individual images of one stack of one channel. However, when I tried to process my files in Watershed I got an error message saying my array and my Bc has different coordinates. I had no idea what is a Bc and how to solve this issue, but I suspected it might be due to my files not being actual stacks any more. I read a few more threads in the forum here and tried to change my image to contain all the stack for each channel and have 4 instead of 32 images. But now, I’m not even able to update my NamesAndTypes section.

Could you please advise me on what exactly am I doing wrong? Thank you very much for the help.

I have attached my project file and my test image.

2.7_LMNA_Nucl_HA-KEKS_a_c1_ORG.tif (8.0 MB) 2.7_LMNA_Nucl_HA-KEKS_a_c2_ORG.tif (8.0 MB) 2.7_LMNA_Nucl_HA-KEKS_a_c3_ORG.tif (8.0 MB) 2.7_LMNA_Nucl_HA-KEKS_a_c4_ORG.tif (8.0 MB)
Nucleolus count project.cpproj (191.3 KB)

1 Like

Hi @M.Anna,

I believe there may be something in your project file that’s become corrupted. If I recreate the pipeline in a fresh window I no longer encounter the errors in NamesAndTypes. I’m not sure what you mean by the ‘Bc’ either, could you post a copy of the full error message?

Hi @M.Anna,

I too tried. I tried with your pipeline, though I couldn’t reproduce the same error it wasn’t loading properly. But I tried as fresh new project file, it worked fine. In the “Metadata” input module I tried to extract the metadata from file headers.
Just FYI, I had used 4 channel .czi file as such it worked fine for me. I think you might have to ensure if the metadata is correct.
Still if not working, as david suggested please post your error.

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

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

Hi,

Thank you for checking it for me. Glad that for once it was not a human error :slight_smile: , it is working fine now. I have also tried to reproduce the Bc error, but since I had to change computers while relocating to home office I was unable to do so.

Thank you again for the help!

Hi,

Thank you for checking it for me as well. I could also extract the metadata from the 4 channel czi file. My problem started when I tried to build a pipeline, since the software was looking for a tiff file. (I uploaded my screenshot)


Which makes me think what is the point being able to even import the file and extract the metadata, since I can not do anything else afterwards :confused: . However, with just making the pipeline in a new window solved my problem with the splitted channels, so I was able to continue building my pipeline.

Thank you for the help!

Hi @M.Anna,

You are Welcome!!!Thanks for sharing screenshot.

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

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