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:
Figure : Sample visualization of atlas (fixed) and moving light sheet microscopy images in 3-D view
Figure : Sample visualization of atlas (fixed), moving and transformed microscopy images after running the registration algorithm
Figure : Sample visualization of atlas (fixed), moving and transformed microscopy images in 2-D coronal view
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
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:
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