I really like when different open-source tools work together nicely in python. To demonstrate this I create the following jupyter notebook: read_czi_analyze_display_heatmap.ipynb
It is combining (among many other things the following tools:
- AICSImageIO and libCZI
- ZEN blue open ANN Specification - to demonstrate that hwo TF2-based networks can be used for segmentation in python (as well as in ZEN)
- scikit-image and (cellpose)[https://pypi.org/project/cellpose/] - as additional segmentation tools
The note basically does the following steps:
- read all the metadata from a CZI file
- read the pixel data “scene-by-scene” - only one at a time!
- segment this image
- measure object parameters
- store them in a table
- display the data as heatmap
… some python code
Feedback is welcome.
Sebi ( from ZEISS)