24 Biomedical Image Analysis and Microscopy
24.1 E-Books and Tutorials
- Bio-image Analysis Notebooks
- Python BioImage Analysis Tutorial
- BIAPy: BioImage Analysis with Python
- Analyzing fluorescence microscopy images with ImageJ
- NEUBIAS Academy
- Grand Challenge: ML in Biomedical Imaging
- Carpenter Lab Public Slides
- Lecture - Applied Bioimage Analysis (2020)
- Deep learning in microscopy collection
- Awesome Cytodata
- CellProfiler Practical: Counting of in situ PLA signals per cell
- SciPy 2021 Bioimage Analysis Fundamentals in Python
- Several image processing workflow examples
- Recommended Readings and Viewings
- BioImage Model Zoo
- deepImageJ
- Bristol: Image analysis courses
- Bioconductor: Basics of image data and spatial patterns analysis in R
- EASY IMAGE PROCESSING IN R USING THE MAGICK PACKAGE
- Bio-Image analysis with Python and Napari - DIGS-BB Light Microscopy Course 2022
- First Principles of Computer Vision
- Data Science in Cell Imaging
- The OpenAI Microscope
- The Journal of Machine Learning for Biomedical Imaging
- CELL TRACKING CHALLENGE
- Bioimage Analysis Course: The Life Cycle of an Image Data Set
- Statistics for Neuroscientists: Image Analysis
- Image Segmentation with Python
24.2 BioImaging Software
- A Hitchhiker’s guide through the bio-image analysis software universe
- ImageScience Software
- DeepLabCut
- DeepLabCut GUI
- Discover, install, and share napari plugins
- napari
- Chan Zuckerberg napari
- StarDist - Object Detection with Star-convex Shapes
- cellfinder-napari
- ilastik
- YAPiC: Yet Another Pixel Classifier (based on deep learning)
- CellPose
- CellProfiler tutorials
- Piximi App
- Piximi GitHuc
- Icy
- nucleAIzer
- ScientiFig
- uList
- ImJoy
- ZeroCostDL4Mic