Read a CZI using libCZI from python scene-by-scene and display heatmap

Hi all,

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:

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

ZEN Experiment:

… some python code

Feedback is welcome.

Sebi ( from ZEISS)