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awesome-scientific-image-analysis
A curated list of scientific image analysis resources and software tools.
https://github.com/epfl-center-for-imaging/awesome-scientific-image-analysis
Last synced: about 8 hours ago
JSON representation
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π Learning resources
- Image data science with Python and Napari - EPFL & TU Dresden
- Image Processing and Analysis for Life Scientists - BIOP, EPFL
- Introduction to Bioimage Analysis - Pete Bankheads
- Microcourses
- Optical microscopy Image Processing & analysis - ->
- Aits Lab - ->
- Did you know β Image Analysis Style - Marie Held -->
- My Journey in Image Analysis - ClΓ udia Salat -->
- Microscopy Series
- Did you know β Image Analysis Style - Marie Held -->
- My Journey in Image Analysis - ClΓ udia Salat -->
- Awesome Biological Image Analysis
- Awesome Computer Vision
- Awesome Medical Imaging
- ImageScience.org - ->
- The Image Analysis Field Guide - EPFL Center for Imaging
- Bio-image Analysis Notebooks - Robert Haase -->
- Introduction to Programming in the Biological Sciences Bootcamp - Justin Bois
- A Hitchhiker's guide through the bio-image analysis software universe - Robert Haase et al.
- Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters
- Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions - Beth Cimini
- Introduction to bioimage analysis
- First principles in computer vision
- DigitalSreeni
- Awesome Biological Image Analysis
- Awesome Computer Vision
- Awesome Medical Imaging
- ImageScience.org - ->
- The Image Analysis Field Guide - EPFL Center for Imaging
- Bio-image Analysis Notebooks - Robert Haase -->
- Introduction to Programming in the Biological Sciences Bootcamp - Justin Bois
- A Hitchhiker's guide through the bio-image analysis software universe - Robert Haase et al.
- Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters
- Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions - Beth Cimini
- Introduction to bioimage analysis
- First principles in computer vision
- DigitalSreeni
- Microscopy Series
- Microcourses
- Optical microscopy Image Processing & analysis - ->
- Aits Lab - ->
-
π Getting started
- Ilastik - Interactive learning and segmentation toolkit
- Napari - A fast and interactive multi-dimensional image viewer for Python
- Setting up Python for scientific image analysis
- Napari - A fast and interactive multi-dimensional image viewer for Python
- QuPath - Open Software for Bioimage Analysis
- Setting up Python for scientific image analysis
- Image data science with Python and Napari - EPFL & TU Dresden
- Image Processing and Analysis for Life Scientists - BIOP, EPFL
- Introduction to Bioimage Analysis - Pete Bankheads
- Fiji - ImageJ, with βbatteries-includedβ
- Ilastik - Interactive learning and segmentation toolkit
-
π§βπ€βπ§ Communities
- Image.sc
- GloBIAS
- SwissBIAS
- Euro-BioImaging - ->
- Image.sc
- GloBIAS
- SwissBIAS
- Euro-BioImaging - ->
- QUAREP-LiMi - ->
- Smart Microscopy - ->
- BIII.eu - ->
- QUAREP-LiMi - ->
- Smart Microscopy - ->
- BIII.eu - ->
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βοΈ Image segmentation
- Thresholding - Introduction to Bioimage Analysis
- Thresholding - Scikit-image
- Segmentation - ImageJ Tutorials
- Image segmentation - Image data science with Python and Napari
- skimage.segmentation
- Ilastik - Pixel Classification
- Segment Anything Model 2 (SAM 2)
- rembg
- nnUNet
- segmentation_models
- segmentation_models.pytorch
- Monai
- StarDist
- CellPose
- pytorch-3dunet - ->
- InstanSeg - ->
- omnipose - ->
- Thresholding - Introduction to Bioimage Analysis
- Thresholding - Scikit-image
- Segmentation - ImageJ Tutorials
- Image segmentation - Image data science with Python and Napari
- skimage.segmentation
- Ilastik - Pixel Classification
- Segment Anything Model 2 (SAM 2)
- Ultralytics YOLO
- rembg
- nnUNet
- segmentation_models
- segmentation_models.pytorch
- Monai
- StarDist
- CellPose
- Detectron2 - ->
- pytorch-3dunet - ->
- InstanSeg - ->
- omnipose - ->
-
π Image registration
- Image correlation - Theory
- ABBA
- pyGPUreg - ->
- Fast4DReg - ->
- SimpleElastix - ->
- DIPY - ->
- ANTsPy - ->
- VoxelMorph - ->
- Image correlation - Practice
- skimage.registration
- SPAM
- pystackreg
- TurboReg
- Warpy
- ABBA
- pyGPUreg - ->
- Fast4DReg - ->
- SimpleElastix - ->
- DIPY - ->
- ANTsPy - ->
- VoxelMorph - ->
- skimage.registration
- pystackreg
- TurboReg
-
πͺ Image denoising
-
π Object detection
-
πΎ Tracking
- Single cell tracking with napari
- Walkthrough (trackpy)
- Getting started with TrackMate
- Trackmate Introduction and Demo - ->
- TrackMate
- Trackpy
- Single cell tracking with napari
- Walkthrough (trackpy)
- Getting started with TrackMate
- Trackmate Introduction and Demo - ->
- TrackMate
- Trackpy
- Trackastra
- ultrack
- co-tracker
- LapTrack
- Trackastra
- ultrack
- co-tracker
- LapTrack
-
π» Visualization
- NeuroMorph
- BigDataViewer
- 3D Slicer - ->
- microfilm - ->
- microviewer - ->
- vizarr - ->
- ndv - ->
- hyperspy - ->
- Visual image comparison (Scikit-image)
- Fiji
- Visual image comparison (Scikit-image)
- Napari
- Neuroglancer
- pyvista
- vedo
- tif2blender
- NeuroMorph
- BigDataViewer
- 3D Slicer - ->
- microfilm - ->
- microviewer - ->
- vizarr - ->
- ndv - ->
- hyperspy - ->
- Napari
- QuPath
- Paraview
- Neuroglancer
- pyvista
- vedo
- tif2blender
Programming Languages
Categories
Sub Categories
Keywords
deep-learning
18
python
16
segmentation
14
image-processing
10
pytorch
10
machine-learning
10
denoising
6
cell-segmentation
6
computer-vision
6
unet
6
visualization
6
pspnet
4
medical-imaging
4
segmentation-models
4
object-detection
4
unet-pytorch
4
semantic-segmentation
4
microscopy-images
4
python3
4
neuroimaging
4
bioimage-analysis
4
microscopy
4
mesh
4
optical-flow
4
image-segmentation
4
blender
4
fpn
4
tracking
4
nuclei-segmentation
2
groupnorm
2
dice-coefficient
2
3d-unet
2
3d-segmentation
2
cell-biology
2
pytorch-3dunet
2
residual-unet
2
volumetric-data
2
bundles
2
contextual-enhancement
2
diffusion-mri
2
dki
2
dti
2
microstructure
2
neuroanatomy
2
patch2self
2
registration
2
self-supervised-learning
2
spherical-harmonics
2
tractography
2
background-removal
2