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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

Jupyter Notebook 36 19 Updated Jul 9, 2024

Your Journey To Fluent Python

Python 1,031 58 Updated Jun 27, 2024

Codebase for "A Foundation Model for Cell Segmentation"

Jupyter Notebook 30 5 Updated Jun 9, 2024

Kipoi's model zoo API

Jupyter Notebook 231 41 Updated Apr 26, 2024

Elephant is the Electrophysiology Analysis Toolkit

Python 189 92 Updated Jul 29, 2024

A hyperparameter optimization framework

Python 10,293 992 Updated Aug 1, 2024

MoSeq2 Jupyter Notebook platform used to run all of the MoSeq2 tools in a GUI.

Python 28 7 Updated May 10, 2024

A platform for compiling, analyzing, and exploring tracking data

Jupyter Notebook 35 3 Updated May 29, 2024

Techniques for deep learning with satellite & aerial imagery

8,210 1,420 Updated Jul 11, 2024

A curated list of softwares, tools, pipelines, plugins etc. for image analysis related to biological questions.

3 Updated May 2, 2024

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

Jupyter Notebook 1,284 372 Updated Jul 29, 2024
Jupyter Notebook 4 2 Updated Apr 26, 2024

Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

Python 148 52 Updated Jul 31, 2024

Image reading, metadata management, and image writing for Microscopy images in Python

Python 21 1 Updated Jul 29, 2024

🎀 Awesome Zarr resources

77 1 Updated Jun 14, 2024

SplineDist: Automated Cell Segmentation with Spline Curves

Jupyter Notebook 64 15 Updated Jun 18, 2024

Bayesian Segmentation of Spatial Transcriptomics Data

Julia 143 29 Updated Jun 18, 2024

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

Python 198 51 Updated Jul 19, 2024
Jupyter Notebook 22 3 Updated Jun 18, 2024

Segmentation error aware clustering for multiplexed imaging

Python 11 2 Updated Jul 31, 2024

SIPEC: the deep-learning Swiss knife for behavioral data analysis

Python 40 6 Updated Apr 5, 2023

Open Source Computer Vision Library

C++ 77,254 55,693 Updated Aug 1, 2024

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

Python 295 54 Updated Jul 28, 2024

Accurate and efficient spot detection for microscopy data

Python 47 4 Updated Jul 29, 2024

Free resources for learning data science

2,879 1,089 Updated Jun 5, 2024

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023

Jupyter Notebook 389 61 Updated Jan 5, 2024

Topological data analysis tool to map microglia morphology along sex- and brain-region-specific spectra

Python 3 2 Updated Mar 19, 2024

Open source Python library for building bioimage analysis pipelines

Jupyter Notebook 118 28 Updated Jul 30, 2024

Minimal Machine Learning Study Plan

1,832 387 Updated Jun 13, 2024

Download FASTQ files from SRA or ENA repositories.

Python 269 24 Updated Aug 11, 2023
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