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NA-MIC Project Weeks

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Loading Large Microscopy Data in Slicer

Key Investigators

Project Description

We’ve developed a module in Slicer - TITAN - that is meant to be an end-to-end pipeline of processing and analyzing imaging mass cytometry data. TITAN allows the user to visualize the different protein channels in the tissue, segment the individual cells in the tissue, and create some simple analysis plots of the data. Currently, user has to export the raw file from the cytometer into TIFF files using an external software in order to use TITAN. However, we would like to use the raw text files directly with Slicer instead, in order to eliminate the need for any external software.


  1. Be able to import large text files into Slicer without causing Slicer to become unresponsive
  2. Update functions in TITAN to work with the text file rather than TIFF images

Approach and Plan

  1. Implement a custom reader to deal with these text files

Progress and Next Steps

  1. Added button to module that opens the user’s file explorer for them to select the text file(s) to be imported
  2. Doing this just points to the file’s location on the computer rather than opening the file in Slicer (which is what slows it down)
  3. Data from the files are obtained by parsing through each line and generating the corresponding image arrays, which are then used to create new volume nodes


Loading text files load text files box

Result of generated image from text file load text files p2

Background and References