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Training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. The material will develop between April and July 2024
Your Journey To Fluent Python
Codebase for "A Foundation Model for Cell Segmentation"
Elephant is the Electrophysiology Analysis Toolkit
MoSeq2 Jupyter Notebook platform used to run all of the MoSeq2 tools in a GUI.
A platform for compiling, analyzing, and exploring tracking data
Techniques for deep learning with satellite & aerial imagery
LSeu-Open / awesome-biological-image-analysis
Forked from hallvaaw/awesome-biological-image-analysisA curated list of softwares, tools, pipelines, plugins etc. for image analysis related to biological questions.
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
Image reading, metadata management, and image writing for Microscopy images in Python
SplineDist: Automated Cell Segmentation with Spline Curves
Bayesian Segmentation of Spatial Transcriptomics Data
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
Segmentation error aware clustering for multiplexed imaging
SIPEC: the deep-learning Swiss knife for behavioral data analysis
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
Accurate and efficient spot detection for microscopy data
Free resources for learning data science
Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
Topological data analysis tool to map microglia morphology along sex- and brain-region-specific spectra
Open source Python library for building bioimage analysis pipelines
Minimal Machine Learning Study Plan
Download FASTQ files from SRA or ENA repositories.