Skip to content

Latest commit

 

History

History
49 lines (37 loc) · 2.9 KB

README.md

File metadata and controls

49 lines (37 loc) · 2.9 KB
Raw

A web-browser-based multidimensional 3D visualizer for confocal and focused-ion beam scanning electron microscopy modalities. Four visualization modules are available: Volume, Surface, Tri-Planar, and Multi-planar reconstruction. Our visualizer takes a sequence of images or stacked image files as input and displays them based on the preferences of the user viewer. For now our visualizer intakes: .dcm, .tif, .tiff, .bmp, .jpg, .mha, .mrc, .nii, .png, .nrrd, .mgh image files as an input.

Features:

  • Volume Rendering (Opacity value slider, Sample distance slider, Blending mode choice, Color choice, Region of intrest clipping slider, Z-dimension scaling)
  • Surface Rendering (Opacity value slider, Iso value slider, Color choice, Region of interest clipping slider, Z-dimension scaling)
  • Tri-Planar Rendering ((XY, YZ, XZ) slider, Color window and level manipulator, Mouse selector (rotate, pan, zoom options))
  • Multi-Planar Reconstruction (Orthoviewer, Separate window for each plane with 3D Image Slice mapper)

Documentation:

https://github.com/Yuvi-416/3D_Visualizer/wiki/3D-Visualizer-Workflow

How to use it?

Demo: https://figshare.com/articles/media/3D-Visualizer_Demo/20408103 More can be found here: https://yuvi-416.github.io/3D_Visualizer/

To host locally:

  • Clone this repository, install latest version of python, and install the packages listed in requirement.txt (by pip install -r requirement.txt).
  • Open the terminal, enter in the folder mpi_vtk_js, and launch the server locally by passing the following command over there: python manage.py runserver
  • And click the localhost link: http://127.0.0.1:8000/

Don't want to host?

If you don't want to host it locally, then copy and paste provided link in any web-browser to use our visualizer. https://yuvi.pythonanywhere.com/

Third-Party Software's:

  • ITK.js
  • VTK.js
  • jQuery
  • Bootstrap
  • Django web framework

Bug and contribution:

  • Found bug? please open an issue or want to contribute please fork it and start to contribute.

Funded:

This work was supported by the Marie Sklodowska Curie ITN-EID, Horizon 2020 project IMAGE-IN (grant agreement No 861122).

If you use this visualizer in your work then please cite below paper:

  • Y. Gupta, R. E. D. Guerrero, C. Costa, R. Jesus, E. Pinho and L. A. Bastião Silva, "Interactive Web-based 3D Viewer for Multidimensional Microscope Imaging Modalities," 2022 26th International Conference Information Visualisation (IV), Vienna, Austria, 2022, pp. 379-384, doi: 10.1109/IV56949.2022.00069.
  • Gupta Y, Costa C, Pinho E, A. Bastião Silva L, Heintzmann R (2022) IMAGE-IN: Interactive web-based multidimensional 3D visualizer for multi-modal microscopy images. PLOS ONE 17(12): e0279825. https://doi.org/10.1371/journal.pone.0279825

License:

This project is under MIT license.