zeiss-microscopy / oad Goto Github PK

Hello Zeiss engineers,

Thank you for the open source repository for the Zen development. I am recently get involved in setting up smart microscopes and image processing on Zeiss products for better integration of existing workflow.

When I comes to the documentation and this repo, the rich content is quite confusing for me to start with, even with the tutorial PDFs.

Would there be a hello world example to show how image can be retrieved from Zen then work with numpy? This will be a great help for the beginners.

If possible can I call custom conda environment as external python?

The two files imgfileutils.py and modules/imgfileutils.py are almost identical, with the exception of some comment lines, see this diff:

https://www.diffchecker.com/MFZsIHQQ

I suggest removing one of the files to avoid version skew and resulting confusion in the future.

Thanks to share this work. I was trying to display my 3D image with napari, you did it !
The jupyter notebook "read and display images using napari " for czi files do not find the colormap for each channel. Is there an issue for that ?
This information doesn't seem to be in he meta data that you show In [11] of the notebook.
I try with my six channels czi image (no time, around 300Mo) , I can open the image but the 3D view have quite a lot of bug to display my image..
Thanks, Mathieu

I apologize if this is explained somewhere else, but I couldn't find it.

I want to write a simple python script using OAD to perform experiment feedback based on the image data. What modules do I need to install on Zen software side to be able to write Python macros in the Macro Editor? When I go to Macro window on the macro editor box is greyed out

Thanks for creating this amazing repo. I have learned so much just by starting at your code. However, I can't run your Jupyter Notebooks. I was wondering if you could provide a requirements.txt file to alleviate my problem. So far I have pip installed all the dependencies but I can't read the czi images because the packages I install are not compatible with each other. I will appreciate any of your help to resolve this problem.

-Frank