In this (first) post, I will be showing how to visualize the data from the proprietary Zeiss LSM (laser scanning microscopy) data format.

  • First, we use MATLAB to manipulate the file, using the bfopen function from bio-formats.
  • Then we save it after properly slicing away the multiple channels (DAPI and Phalloidin) into two distinct arrays.
  • These files are then loaded into Python, where k3d and vedo (a most recommended visualization toolkit!) are used to visualize the data.

Check out the MATLAB/Python repository for the details on how this extraction and visualization is done.

Click here (or on the image below) to enter the interactive 2-channel model for an example nodule of cancer cells (courtesy of Dr. Jonathan Celli here at UMass Boston). Use the dropdown menu to toggle visibility of the two channels, and alter the minimum thresholds (vmin).


Please file all bugs/feature requests at repo.