Python (65)#
2022 MIC Workshop on Bioimage processing with Python#
[‘Guillaume Witz’]
Licensed UNKNOWN
Tags: Python, Bioimage Analysis
Content type: Notebook
Annotating 3D images in napari#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/03/30/annotating-3d-images-in-napari/
BIDS-lecture-2024#
[‘Robert Haase’]
Licensed CC-BY-4.0
Training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. The material developed here between April and July 2024.
Tags: Bioimage Analysis, Deep Learning, Microscopy Image Analysis, Python
Content type: Github Repository
BiaPy: Bioimage analysis pipelines in Python#
[‘Daniel Franco-Barranco’, ‘et al.’]
BiaPy is an open source Python library for building bioimage analysis pipelines, also called workflows.
Tags: Workflow Engine, Python
Content type: Documentation
Bio-image Analysis with the Help of Large Language Models#
[‘Robert Haase’]
Published 2024-03-13
Licensed CC-BY-4.0
Large Language Models (LLMs) change the way how we use computers. This also has impact on the bio-image analysis community. We can generate code that analyzes biomedical image data if we ask the right prompts. This talk outlines introduces basic principles, explains prompt engineering and how to apply it to bio-image analysis. We also compare how different LLM vendors perform on code generation tasks and which challenges are ahead for the bio-image analysis community.
Tags: Large Language Models, Python
Content type: Slide
Bio-image Data Science#
[‘Robert Haase’]
Licensed CC-BY-4.0
This repository contains training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python.
Tags: Image Data Management, Deep Learning, Microscopy Image Analysis, Python
Content type: Notebook
Bio-image Data Science Lectures @ Uni Leipzig / ScaDS.AI#
[‘Robert Haase’]
Licensed CC-BY-4.0
These are the PPTx training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. The material developed here between April and July 2024.
Tags: Bioimage Analysis, Deep Learning, Microscopy Image Analysis, Python
Content type: Slides
Bio-image analysis, biostatistics, programming and machine learning for computational biology#
[‘Anna Poetsch’, ‘Biotec Dresden’, ‘Marcelo Leomil Zoccoler’, ‘Johannes Richard Müller’, ‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis, Napari
Content type: Notebook
BioEngine Documentation#
[‘Wei Ouyang’, ‘Nanguage’, ‘Jeremy Metz’, ‘Craig Russell’]
Licensed MIT
BioEngine, a Python package designed for flexible deployment and execution of bioimage analysis models and workflows using AI, accessible via HTTP API and RPC.
Tags: Workflow Engine, Deep Learning, Python
Content type: Documentation
BioImage Analysis Notebooks#
[‘Robert Haase et al.’]
Licensed [‘CC-BY-4.0’, ‘BSD-3-CLAUSE’]
Tags: Python, Bioimage Analysis
Content type: Book, Notebook
https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html
Bioimage analysis with Napari#
[‘Fabrizio Musacchio’]
Licensed CC-BY-ND-SA-4.0
Tags: Python, Napari, Bioimage Analysis
Content type: Collection
https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/
Browsing the Open Microscopy Image Data Resource with Python#
[‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Omero, Python
Content type: Blog
https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html
CARE/Stardist tutorials for EMBO Practical Course — Computational optical biology 2022#
[‘Martin Weigert’]
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
CSBDeep and StarDist @ I2K 2020#
[‘Martin Weigert’, ‘Uwe Schmidt’]
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
Chris Halvin YouTube channel#
Licensed UNKNOWN
Tags: Napari, Python, Bioimage Analysis
Content type: Collection, Video
https://www.youtube.com/@chrishavlin
https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1
Course on Deep Learning for imaging using PyTorch#
[‘Guillaume Witz’]
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Artificial Intelligence
Content type: Notebook
Dask Course#
[‘Guillaume Witz’]
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Big Data
Content type: Notebook
Deep Learning Based Segmentation For Biologists#
Licensed AGPL-3.0
Tags: Python, R, Artificial Intelligence
Content type: Notebook
Deep Vision and Graphics#
[‘Victor Yurchenko’, ‘Fedor Ratnikov’, ‘Viktoriia Checkalina’]
Licensed MIT
Tags: Python, Artificial Intelligence
Content type: Notebook
DigitalSreeni YouTube Channel#
[‘Sreeni Bhattiprolu’]
A collection tutorial videos for using Python in general and for processing images using Python, machine learning and deep learning
Tags: Python
Content type: Collection, Video
EMBL Deep Learning course 2019 exercises and materials#
[‘Valentyna Zinchenko’, ‘Pejman Rasti’, ‘Martin Weigert’, ‘Szymon Stoma’]
Licensed UNKNOWN
Tags: Python, Artificial Intelligence
Content type: Notebook
EMBL Deep Learning course 2021/22 exercises and materials#
[‘Martin Weigert’, ‘Constantin Pape’]
Licensed UNKNOWN
Tags: Python, Artificial Intelligence
Content type: Notebook
EMBL Deep Learning course 2023 exercises and materials#
[‘Martin Weigert’, ‘Uwe Schmidt’, ‘Benjamin Gallusser’, ‘Albert Dominguez Mantes’, ‘Buglakova Alyona’]
Licensed UNKNOWN
Tags: Python, Artificial Intelligence
Content type: Notebook
Feature extraction in napari#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/05/03/feature-extraction-in-napari/
Fractal Documentation#
Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization.
Tags: Workflow Engine, Python
Content type: Documentation
Fundamentals of image analysis in Python with scikit-image, napari, and friends#
[‘Juan Nunez-Iglesias’]
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis
Content type: Notebook
Generative artificial intelligence for bio-image analysis#
[‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis, Artificial Intelligence
Content type: Slide
Getting started with Mambaforge and Python#
[‘Mara Lampert’]
Licensed CC-BY-4.0
Tags: Python, Conda, Mamba
Content type: Blog
https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html
How to write a bug report#
[‘Mara Lampert’]
Tags: Github, Python, Science Communication
Content type: Blog
https://focalplane.biologists.com/2024/04/03/how-to-write-a-bug-report/
Image analysis and visualization in Python with scikit-image, napari, and friends#
[‘Juan Nunez-Iglesias’]
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis
Content type: Notebook
Image processing for beginners#
[‘Guillaume Witz’]
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis
Content type: Notebook
Image processing with Python#
[‘Guillaume Witz’]
Licensed MIT
Series of Notebooks exposing how to do mostly basic and some advanced image processing using Python. It uses standard packages (Numpy, Maplotlib) and for the image processing parts is heavily based on the scikit-image package.
Tags: Python
Content type: Notebook
Introduction to Bioimage Analysis#
[‘Pete Bankhead’]
Licensed CC-BY-4.0
Tags: Python, Imagej, Bioimage Analysis
Content type: Book, Notebook
Introduction to Deep Learning for Microscopy#
[‘Costantin Pape’]
Licensed MIT
This course consists of lectures and exercises that teach the background of deep learning for image analysis and show applications to classification and segmentation analysis problems.
Tags: Deep Learning, Pytorch, Segmentation, Python
Content type: Notebook
Making your package available on conda-forge#
[‘Kevin Yamauchi’]
Licensed CC-BY-4.0
Tags: Deployment, Python
Content type: Documentation
https://kevinyamauchi.github.io/open-image-data/how_tos/conda_forge_packaging.html
Managing Scientific Python environments using Conda, Mamba and friends#
[‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Python, Conda, Mamba
Content type: Blog
Materials for EMBL Coding Club Mini-Tutorials#
[‘Jonas Hartmann’, ‘et al.’]
Licensed UNKNOWN
Tags: Python
Content type: Code, Notebook
Metabolic networks modelling with COBRApy#
[‘Karin Sasaki’, ‘Aleksej Zelezniak’]
Licensed UNKNOWN
Tags: Python
Content type: Notebook
Microscopy data analysis: machine learning and the BioImage Archive#
[‘Andrii Iudin’, ‘Anna Foix-Romero’, ‘Anna Kreshuk’, ‘Awais Athar’, ‘Beth Cimini’, ‘Dominik Kutra’, ‘Estibalis Gomez de Mariscal’, ‘Frances Wong’, ‘Guillaume Jacquemet’, ‘Kedar Narayan’, ‘Martin Weigert’, ‘Nodar Gogoberidze’, ‘Osman Salih’, ‘Petr Walczysko’, ‘Ryan Conrad’, ‘Simone Weyend’, ‘Sriram Sundar Somasundharam’, ‘Suganya Sivagurunathan’, ‘Ugis Sarkans’]
Licensed CC-BY-4.0
The Microscopy data analysis: machine learning and the BioImage Archive course, which focused on introducing programmatic approaches used in the analysis of bioimage data via the BioImage Archive, ran in May 2023.
Tags: Microscopy Image Analysis, Python, Deep Learning
Content type: Videos, Practicals, Slides
NEUBIAS Academy @HOME: Interactive Bioimage Analysis with Python and Jupyter#
Licensed BSD-3-CLAUSE
Tags: Python, Neubias, Bioimage Analysis
Content type: Notebook
NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon)#
[‘Mohamed M. Abdrabbou’, ‘Mehrnaz Babaki’, ‘Tom Boissonnet’, ‘Michele Bortolomeazzi’, ‘Eik Dahms’, ‘Vanessa A. F. Fuchs’, ‘Moritz Hoevels’, ‘Niraj Kandpal’, ‘Christoph Möhl’, ‘Joshua A. Moore’, ‘Astrid Schauss’, ‘Andrea Schrader’, ‘Torsten Stöter’, ‘Julia Thönnißen’, ‘Monica Valencia-S.’, ‘H. Lukas Weil’, ‘Jens Wendt and Peter Zentis’]
Licensed CC-BY-4.0
Tags: Arc, Dataplant, Hackathon, Nfdi4Bioimage, Omero, Python, Research Data Management
Content type: Event, Publication, Documentation
Neubias Academy 2020: Introduction to Nuclei Segmentation with StarDist#
[‘Martin Weigert’, ‘Olivier Burri’, ‘Siân Culley’, ‘Uwe Schmidt’]
Licensed UNKNOWN
Tags: Python, Neubias, Artificial Intelligence, Bioimage Analysis
Content type: Slide, Notebook
NextFlow core#
nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow
Tags: Python
Content type: Collection
OMERO - HCS analysis pipeline using Jupyter Notebooks#
[‘Riccardo Massei’]
Licensed MIT
Material and solutions for the course ‘Bioimage data management and analysis with OMERO’ held in Heidelberg (13th May 2024) - Module 3 (1.45 pm - 3.45 pm): OMERO and Jupyter Notebooks. Main goal of the workflow is to show the potential of JN to perform reproducible image analysis in connection with an OMERO instance. In this specific example, we are performing a simple nuclei segmentation from raw images uploaded in OMERO.
Tags: Teaching, Bioimage Analysis, Notebooks, Python, Omero
Content type: Github Repository
ONBI Image Analysis Course#
[‘Mark Jenkinson’, ‘Jens Rittscher’, ‘Dominic Waithe’]
Licensed GPL-2.0
This repository contains the materials for the University of Oxford DTC ONBI Image Analysis course.
Tags: Python, Bioimage Analysis
Content type: Notebook
Open Image Data Handbook#
[‘Kevin Yamauchi’]
Licensed CC-BY-4.0
Tags: Neubias, Research Data Management, Napari, Python, Bioimage Analysis
Content type: Book, Notebook
PoL Bio-Image Analysis Early Career Bio-image Analysis Training School#
Tags: Bioimage Analysis, Python
Content type: Event, Notebook
https://biapol.github.io/PoL-BioImage-Analysis-TS-Early-Career-Track/intro.html
PoL Bio-Image Analysis GPU Accelerated Image Analysis Training School#
Tags: Bioimage Analysis, Python
Content type: Event, Notebook
https://biapol.github.io/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis/intro.html
PoL Bio-Image Analysis Training School on GPU-Accelerated Image Analysis#
[‘Stephane Rigaud’, ‘Brian Northan’, ‘Till Korten’, ‘Neringa Jurenaite’, ‘Apurv Deepak Kulkarni’, ‘Peter Steinbach’, ‘Sebastian Starke’, ‘Johannes Soltwedel’, ‘Marvin Albert’, ‘Robert Haase’]
Licensed CC-BY-4.0
This repository hosts notebooks, information and data for the GPU-Accelerated Image Analysis Track of the PoL Bio-Image Analysis Symposium.
Tags: Gpu, Clesperanto, Dask, Python
Content type: Notebook
BiAPoL/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis
Prompt Engineering in Bio-image Analysis#
[‘Mara Lampert’]
Tags: Python, Jupyter, Bioimage Analysis, Prompt Engineering, Biabob
Content type: Blog
https://focalplane.biologists.com/2024/07/18/prompt-engineering-in-bio-image-analysis/
Python BioImage Analysis Tutorial#
[‘Jonas Hartmann’]
Licensed MIT
Tags: Python, Bioimage Analysis
Python Workshop - Image Processing#
[‘Karin Sasaki’, ‘Jonas Hartmann’]
Licensed UNKNOWN
Tags: Python
Content type: Code, Notebook
Python for Microscopists#
[‘Sreenivas Bhattiprolu’]
Licensed MIT
Tags: Python, Bioimage Analysis
Content type: Notebook, Collection
QI 2024 Analysis Lab Manual#
[‘Beth Cimini’, ‘Florian Jug’, ‘QI 2024’]
Licensed CC-BY-4.0
This book contains the quantitative analysis labs for the QI CSHL course, 2024
Tags: Segmentation, Python
Content type: Notebook
https://bethac07.github.io/qi_2024_analysis_lab_manual/intro.html
QM Course Lectures on Bio-Image Analysis with napari 2024#
[‘Marcelo Leomil Zoccoler’]
Licensed CC-BY-4.0
In these lectures, we will explore ways to analyze microscopy images with Python and visualize them with napari, an nD viewer open-source software. The analysis will be done in Python mostly using the scikit-image, pyclesperanto and apoc libraries, via Jupyter notebooks. We will also explore some napari plugins as an interactive and convenient alternative way of performing these analysis, especially the napari-assistant, napari-apoc and napari-flim-phasor-plotter plugins.
Tags: Napari, Python
Content type: Notebook
https://zoccoler.github.io/QM_Course_Bio_Image_Analysis_with_napari_2024
Quality assurance of segmentation results#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/04/13/quality-assurance-of-segmentation-results/
Rescaling images and pixel (an)isotropy#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/03/02/rescaling-images-and-pixel-anisotropy/
Running Deep-Learning Scripts in the BiA-PoL Omero Server#
[‘Marcelo Zoccoler’]
Licensed CC-BY-4.0
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Blog
https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html
Scientific Visualization: Python + Matplotlib#
[‘Nicolas P. Rougier’]
Licensed CC-BY-ND-SA-4.0
Tags: Python
Content type: Book
Snakemake Documentation#
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
Tags: Workflow Engine, Python
Content type: Documentation
https://snakemake.readthedocs.io/en/stable/
https://academic.oup.com/bioinformatics/article/28/19/2520/290322
SpatialData: an open and universal data framework for spatial omics#
[‘Luca Marconato’, ‘Giovanni Palla’, ‘Kevin A Yamauchi’, ‘Isaac Virshup’, ‘Elyas Heidari’, ‘Tim Treis’, ‘Marcella Toth’, ‘Rahul Shrestha’, ‘Harald Vöhringer’, ‘Wolfgang Huber’, ‘Moritz Gerstung’, ‘Josh Moore’, ‘Fabian J Theis’, ‘Oliver Stegle’]
Licensed CC-BY-4.0
Tags: Python
Content type: Publication, Preprint
https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1.abstract
Teaching Bioimage Analysis with Python#
[‘Rafael Camacho’]
Licensed MIT
Tags: Python, Bioimage Analysis
Content type: Tutorial
Tracking in napari#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/06/01/tracking-in-napari/
ZEN & Python workshop#
Licensed GPL-3.0
Tags: Python, Napari, Bioimage Analysis
Content type: Collection, Notebook
numpy pandas course#
[‘Guillaume Witz’]
Licensed BSD-3-CLAUSE
Tags: Python
Content type: Notebook