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NA-MIC Project Weeks

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Visualizing mass spectomatry data using Slicer

Key Investigators

Project Description

Our project aims to develop a Slicer module, called ViPRE, an open-source software for analysis of Mass Spectrometry imaging data. ViPRE allows users to input DESI (Desorption electrospray ionization) data and visualize it in PCA (Principal Components Analysis) or single ion imaging. It also enables you to upload histopathology images for correspondence. Currently, we want to allow users to visualize a plot of the mass spectrum for each pixel imaging. We would also like to enable users to do image segmentation within the module. As of now, you need to open the image segmentation module to segment your tissue image.


  1. Objective A. Be able to plot a mass spectrum graph when clicking a pixel on the PCA image generated by the Slicer module
  2. Objective B. Enable users to segment their PCA images within the module instead of having to switch to the image segmentation module in Slicer

Approach and Plan

  1. Create a function that plots the mass spectrum and displays it on Slicer
  2. The current issue is that the function is unable to access the peaks. This results with a plot with no bars
  3. Create a function that takes cursor coordinates in real time and saves them if the user clicks on the pixel
  4. Add the segmentation properties to the ViPRE module

Progress and Next Steps

  1. I have already created a function that takes cursor coordinates in real time and saves them when the user presses the “.” button on their keyboard


Screen Shot 2022-06-26 at 2 41 55 PM

Background and References