Papers

• 2023 - Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters.
• 2023 - Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters.
• 2022 - A Hitchhiker's guide through the bio-image analysis software universe - Robert Haase et al.
• 2023 - Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters.
• 2023 - Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters.
• 2024 - Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions - Beth Cimini.
• 2023 - Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters.

• Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters
• Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters
• Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters
• Microcourses
• Optical microscopy Image Processing & analysis - ->
• Aits Lab - ->
• Did you know – Image Analysis Style - Marie Held -->
• My Journey in Image Analysis - Clàudia Salat -->
• 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
• Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters
• 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 - ->
• Towards effective adoption of novel image analysis methods - Talley Lambert, Jennifer Waters

Video series

• Did you know – Image Analysis Style - Marie Held -->
• My Journey in Image Analysis - Clàudia Salat -->

Curated lists

• Awesome Biological Image Analysis
• Awesome Computer Vision
• Awesome Medical Imaging

Reproducibility

• When seeing is not believing: application-appropriate validation matters for quantitative bioimage analysis
• Reproducible image handling and analysis
• Understanding metric-related pitfalls in image analysis validation
• Reporting reproducible imaging protocols
• When seeing is not believing: application-appropriate validation matters for quantitative bioimage analysis
• Processing images for papers & posters - ->
• When seeing is not believing: application-appropriate validation matters for quantitative bioimage analysis
• When seeing is not believing: application-appropriate validation matters for quantitative bioimage analysis

Software development practices

• The Turing Way handbook
• Code Publishing cheat sheet

Figures creation

• Community-developed checklists for publishing images and image analysis
• Creating Clear and Informative Image-based Figures for Scientific Publications
• Effective image visualization for publications – a workflow using open access tools and concepts
• Publishing images for papers & posters - ->

Software tools

• skimage.segmentation - Classical segmentation algorithms in Python.
• Ilastik - Pixel Classification - Semi-supervised workflow for pixel classification.
• Segment Anything Model 2 (SAM 2) - Promptable, foundation model for image segmentation.
• rembg - Remove image backgrounds.
• nnUNet - U-Net based biomedical image segmentation (2D and 3D).
• segmentation_models - Segmentation models with pretrained backbones in Keras (Tensorflow).
• segmentation_models.pytorch - Segmentation models with pretrained backbones in Pytorch.
• Monai - Pytorch-based deep learning framework for biomedical imaging.
• StarDist - Segmentation of cell nuclei and other round (star-convex) objects.
• pytorch-3dunet - ->
• InstanSeg - ->
• omnipose - ->
• SAMJ - Segment Anything in Fiji.
• YOLO11 - Instance Segmentation - Image segmentation using Ultralytics YOLO.
• CellPose - Segmentation of cells and membranes in microscopy images.

Learning resources

• Thresholding - Introduction to Bioimage Analysis
• Thresholding - Scikit-image - ->
• Segmentation - ImageJ Tutorials - ->
• Image segmentation - Image data science with Python and Napari

• 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 - ->

Learning resources

• Image correlation - Practice
• Image correlation - Theory

Software tools

• pyGPUreg - ->
• Fast4DReg - ->
• SimpleElastix - ->
• DIPY - ->
• ANTsPy - ->
• VoxelMorph - ->
• ABBA - Aligning Big Brains and Atlases.
• skimage.registration - Cross-correlation and optical flow algorithms in Python.
• SPAM - Image correlation in 2D and 3D.
• pystackreg - Image stack (or movie) alignment in Python.
• TurboReg - Image stack (or movie) alignment in Fiji.
• Warpy - Register whole slide images in Fiji.

• Image correlation - Theory
• Image correlation - Practice
• ABBA
• pyGPUreg - ->
• Fast4DReg - ->
• SimpleElastix - ->
• DIPY - ->
• ANTsPy - ->
• VoxelMorph - ->
• skimage.registration
• pystackreg
• TurboReg

Learning resources

• Noise - Introduction to Bioimage Analysis
• Denoising a picture (scikit-image)

Software tools

• SwinIR - Deep image restoration using Swin Transformer - for grayscale and color images.
• noise2self - Blind denoising with self-supervision.
• CellPose3 - OneClick - Deep-learning based denoising models for fluorescence and microscopy images.
• CSBDeep - Image restoration in Fiji.
• skimage.restoration - Classical denoising algorithms in Python (TV Chambolle, Non-local Means, etc.).
• CAREamics - Deep-learning based, self-supervised algorithms: Noise2Void, N2V2, etc.

• Noise - Introduction to Bioimage Analysis
• Denoising a picture (scikit-image)
• Noise2Void - ->
• Aydin - ->
• skimage.restoration
• CAREamics
• Noise2Void - ->
• Aydin - ->

Software tools

• DeepLabCut - Animal pose estimation.
• OpenPifPaf - Human pose estimation.
• Spotiflow - Spot detection for microscopy data.
• Detectron2 - ->
• YOLO11 - Object Detection - Object detection using Ultralytics YOLO.

• Ultralytics YOLO
• DeepLabCut
• OpenPifPaf
• Spotiflow
• Detectron2 - ->

Learning resources

• Single cell tracking with napari
• Walkthrough (trackpy)
• Getting started with TrackMate
• Trackmate Introduction and Demo - ->

Software tools

• TrackMate - Fiji plugin.
• Trackpy - Particle tracking in Python.
• Mastodon - Large-scale tracking in Fiji.
• Trackastra - Tracking with Transformers.
• ultrack - Large-scale cell tracking.
• co-tracker - Tracking any point on a video.
• LapTrack - Particle tracking in Python.

• Single cell tracking with napari
• Walkthrough (trackpy)
• Getting started with TrackMate
• Trackmate Introduction and Demo - ->
• TrackMate
• Trackpy
• Trackastra
• ultrack
• co-tracker
• LapTrack

Software tools

• Napari - Interactive nD image viewer in Python
• Neuroglancer - Browser-based visualizations compatible with large images (zarr)
• PyVista - 3D visualizations in Python through VTK
• vedo - Scientific visualizations of 3D objects
• Fiji - Volume Viewer - Ideal for Fiji users
• Fiji - 3D Viewer - Ideal for Fiji users
• Fiji - 3Dscript - 3D rendering animations in Fiji
• Viv - Multiscale visualization on the web
• supervision - ->
• fastplotlib - ->
• K3D-jupyter - ->
• itkwidgets - VTK viewer in Jupyter notebooks
• ipyvtklink - ->
• ipyvolume - ->
• ipygany - ->
• NeuroMorph - ->
• Fiji - BigDataViewer - Ideal for big data
• 3D Slicer - ->
• microfilm - ->
• microviewer - ->
• vizarr - Simple Zarr viewer
• ndv - ->
• hyperspy - ->
• Paraview - Scientific visualizations through VTK

Learning resources

• Visual image comparison (Scikit-image)

• Visual image comparison (Scikit-image)
• tif2blender
• NeuroMorph
• BigDataViewer
• 3D Slicer - ->
• microfilm - ->
• microviewer - ->
• vizarr - ->
• ndv - ->
• hyperspy - ->
• Napari
• QuPath
• Neuroglancer
• pyvista
• vedo
• tif2blender

Learning resources

• System aspects - Basics of Computing Environments for Scientists
• Accelerated large-scale image procesing in Python

Software tools

• pyclesperanto_prototype - GPU-accelerated bioimage analysis.
• Numba - JIT compiler for Python and Numpy code.
• cuCIM - GPU-accelerated image processing.
• OpenCV - Optimized image processing algorithms.

Python setup

• Managing Conda Environments
• Conda Cheatsheet - ->
• Python environments workshop - Talley Lambert.
• Setting up Python for scientific image analysis - ->

Python programming

• Python 3 documentation
• Automate the Boring Stuff with Python - ->
• Programming with Python - Software Carpentry.
• pydevtips: Python Development Tips - Eric Bezzam. -->
• Python packaging 101 - ->

Python for image processing

• Image processing with Python - Guillaume Witz. -->
• Scikit-image - Scientific image processing toolbox.
• 3.3. Scikit-image: image processing - Scientific Python Lectures. -->
• scipy.ndimage - Multidimensional image processing.
• opencv-python - Computer vision toolbox.

Learning resources

• Scientific Imaging Tutorials - ImageJ.
• Image handling using Fiji - training materials - Joanna Pylvänäinen.
• Fiji Programming Tutorial - ->

Plugins

• ThunderSTORM
• MorphoLibJ - Morphological operations.
• DeepImageJ - Run deep learning models in Fiji.

Plugins

• napari hub
• napari-skimage-regionprops - Region properties.
• napari-threedee - 3D interactivity toolbox.
• Omega - Napari with ChatGPT.
• napari-sam - Segment Anything in Napari.
• napari-imagej - Fiji in Napari.
• devbio-napari - Comprehensive image processing toolbox.
• napari-clusters-plotter - Object clustering.
• napari-accelerated-pixel-and-object-classification - Semi-supervised pixel classification.
• Usage (napari.org)
• napari-animation - Create animations.
• napari-convpaint - Pixel classification based on deep learning feature extraction.

Extensions

• qupath-extension-sam - Segment Anything in QuPath.
• qupath-extension-cellpose - CellPose.
• qupath-extension-stardist - StarDist.

Plugins

• QuPath Documentation

Extensions

• BIOP-desktop - Virtual desktop for bioimage analysis.
• BAND - Bioimage ANalysis Desktop.
• Fractal - Framework to process bioimaging data at scale in the OME-Zarr format.
• Galaxy (EU) - Web-based platform for accessible computational research.
• Renkulab - Data, Code, and Compute all under one roof.
• Hugging Face Spaces - Build, host, and share ML apps.
• BioImage.IO dev - Models, Datasets, and Applications for bioimage analysis.

🤖 LLMs

• bia-bob
• BioImage.IO Chatbot

📷 Image acquisition

• Cameras and Lenses - Bartosz Ciechanowski.
• Knowledge Center - Edmund Optics.
• Guides - Center for Microscopy and Image Analysis - University of Zurich -->

🩻 Image reconstruction

• Pyxu - Modular and Scalable Computational Imaging.
• Welcome to Inverse Problems and Imaging - ->

💲 Splines

• SplineBox - Efficient splines fitting in Python.

🍭 Orientation

• OrientationJ - Fiji plugin.
• OrientationPy - 2D and 3D orientation measurements in Python.

🛠️ Utilities

• aicsimageio - Image reading and metadata conversion.
• imageio - Python library for reading and writing image data.
• patchify - Image patching (tiling).
• pims - Python Image Sequence.
• imutils - Image utilities.
• imantics - Image annotation semantics (Masks, Bounding Box, Polygons...) -->
• ncolor - Remapping of instance labels -->
• Depth Anything - ->
• pixelflow - ->