Misc

• Papers
  • Comparison of Three 3D Segmentation Software Tools for Hip Surgical Planning - PMC: compares 3d slicer, Syngo, and Materialize¹
    • 
  • Comprehensive Review of 3D Segmentation Software Tools for MRI Usable for Pelvic Surgery Planning - PMC²: 12 software tools
    • really nice criteria, incl. extensibility etc.
    • 
    • 
    • TL;DR: ITK-SNAP most usable, Myrian Studio second but windows-only, 3d Slicer third but neat because easily extendable. Seg3d as also mentioned as aving very good usability
• Misc
  • https://github.com/neurolabusc/niivue-images sample nii images for evaluating nii viewers/editors

+ 3d Slicer

• Main file: 240715-1653 Notes on 3d-slicer, 240718-1530 First python 3d slicer interactions
• License:
  • About 3D Slicer — 3D Slicer documentation
  • custom license: BSD-style, broadly open source
    • no GPL/copyleft code allowed because it’d make it harder to mix slicer w/ private intellectual property
    • commercial use OK
    • 3d slicer based products — only some are listed, because one can use it and not disclose it and it’s fine
• Language: python
• extensible in python as well
  • has many cool extensions: @KitwareMedical/slicer-extensions-webapp
  • includes MONAILabel active learning extension plugin
  • a whole category for developer tools! @KitwareMedical/slicer-extensions-webapp
  • Extension Wizard — 3D Slicer documentation
    • https://extensions.slicer.org/catalog/Shape Analysis/32952/linux has extensions about stats
  • ai-assisted-annotation-client/slicer-plugin/README.md at master · NVIDIA/ai-assisted-annotation-client
• Very active community and frequent updates
• Downsides
  • J:
    • too specific for medical images
    • presets hard to customize (I agree!)
    • bad documentation (I think fixed now)
  • but: “Best of the free ones”
• Ha: https://github.com/NVIDIA/ai-assisted-annotation-client/blob/master/slicer-plugin/README.md

+ Syngo

• syngo.via OpenApps – Siemens Healthineers Deutschland
• Paid.
• Best according to ¹
• No easy way to test.

MeVisLab

• https://www.mevislab.de/
• Commercial and non-commercial version available
• Documentation:
  • Getting Started
• SDK for scripting exists
  • python QT bindings available
  • and generally feels expandable w/ python, shows python errors in the main screen for example, which is a good sign
• Official video tutorials exist, incl. for application development: MeVisLab - YouTube
• Download: a single .bin file that has to be run
• I don’t really like the website but the program itself feels nice!
• Nice pipeline visualization: and adding blocks — much less chaotic than 3d slicer (at first glance)
• overall good impression
• python scripting has a nice reference etc.

ITK-SNAP

• TODO
• Winner of ² due to its usability, does segmentation only but does it well
• available on AUR
• tutorial: TutorialSectionVolumes
• I really like it as first impression
• Has a distributed segmentation service already implemented!
  • ITK-SNAP Distributed Segmentation Services
  • 
  • ASHS Documentation - Overview sample of such a service
  • (can’t test it because pyqt6 present but not found)
• has volumes and statistics, maybe expandable
• BUT can’t find easy ways to add plugins

+ 3D Seg

• Open Source, segmentation-first
• for linux has to be compiled from source
• last meaningful commits from ~3 years ago: Commits · SCIInstitute/Seg3D, last release 2021 as well
• tried to build it, as ./build, failed because can’t find svn for
• Has detailed-ish developer documentation as videos! https://www.sci.utah.edu/cibc-software/seg3d.html
• Couldn’t build locally sadly, error in the middle of it
• Giving up

Myrian

• commercial, but non-commercial exists, and can be extended with plugins

NeuroMorph

• NeuroMorph ‐ EPFL
  • NeuroMorph | BIII
• Blender-based!

• NeuroMorph is a set of tools designed to import, analyze, and visualize mesh models in Blender. It has been developed specifically for the morphological analysis of 3D objects derived from serial electron microscopy images of brain tissue, but much of its functionality can be applied to any 3D mesh.

ilastic

• ilastik - ilastik
• integrat-able with fiji: ilastik/ilastik4ij: ImageJ plugins to run ilastik workflows and with everything else
• BioImage.IO integration as well, btw another model zoo

Fiji

• Fiji: ImageJ, with “Batteries Included”
• Legendary
• infinite plugins, very well known, downloadable as executable
• not too easy to use in my subjective opinion, menus inside menus, but…

Kitware glance

https://kitware.github.io/glance/doc/index.html

• web-based, extendable
• Kitware/glance: Kitware Glance is an open-source web application developed at Kitware for visualizing volumetric images, molecular structures, geometric objects, and point clouds. It is part of the ParaView platform and can serve as a foundation for building custom web-based visualization applications involving ITK.js and VTK.js.

Biaflows

• https://biaflows-sandbox.neubias.org/#/
• fully-online and can run models
• I don’t like the 3d viewer and I think it’s segmentation only, no easy way to generate/show stats