DenizDogan92 / Microscopy_Image_Analysis_Software

Desktop Application for the analysis of volumetric microscopy or medical image data

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Microscopy Image Analysis Software

Desktop application that allows you to view and analyze volumetric microscopy or medical image data. Currently, the application has the following features:

  • Visualization of volumetric data in 2-D and 3-D views
  • Automated image registration with various transformations

The following main packages and libraries have been utilized for the implementation of the software:

  • PyQt5 for the GUI widgets
  • vtk for the visualization of the volumetric image data
  • ants for the computations and image registration algorithm

As the future work, following new features can be added to the software:

  • Preprocessing operations on volumetric images
  • Automated segmentation of volumetric images

Here are some screenshots I take from this GUI software:

image_analysis_gui_screenshot2

Figure : Sample visualization of atlas (fixed) and moving light sheet microscopy images in 3-D view

image_analysis_gui_screenshot3

Figure : Sample visualization of atlas (fixed), moving and transformed microscopy images after running the registration algorithm

image_analysis_gui_screenshot4

Figure : Sample visualization of atlas (fixed), moving and transformed microscopy images in 2-D coronal view

Libraries:

Here is the full list of libraries that I have used in this software:

  • ants
  • numpy
  • tifffile
  • PyQt5
  • vtk

All of them can be installed via pip package manager

How to Run:

After installing the required packages, simply run the imaging_gui.py and it will open the following window where you can select your fixed (atlas) and moving image files:

image_analysis_gui_screenshot1

​ Figure : Initial window

After you select your images, the software will render the images in 3-D view and allow you to run the registration algorithm

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Desktop Application for the analysis of volumetric microscopy or medical image data


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Language:Python 100.0%