Github repository (35)#
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
Biomero#
Torec Luik, Johannes Soltwedel
Published 2024-07-24
Licensed APACHE-2.0
The BIOMERO framework, for BioImage analysis in OMERO, allows you to run (FAIR) bioimage analysis workflows directly from OMERO on a high-performance compute (HPC) cluster, remotely through SSH.
Tags: OMERO, Github
Content type: Github Repository
EmbedSeg Repository#
Manan Lalit, Joran Deschamps, Florian Jug, Ajinkya Kulkarni
Licensed CC-BY-NC-4.0
Code Implementation for EmbedSeg, an Instance Segmentation Method for Microscopy Images
Tags: Bioimage Analysis, Instance Segmentation
Content type: Github Repository
Example Pipeline Tutorial#
Tim Monko
Published 2024-10-28
Licensed BSD-3-CLAUSE
Napari-ndev is a collection of widgets intended to serve any person seeking to process microscopy images from start to finish. The goal of this example pipeline is to get the user familiar with working with napari-ndev for batch processing and reproducibility (view Image Utilities and Workflow Widget).
Tags: Napari, Microscopy Image Analysis, Bioimage Analysis
Content type: Documentation, Github Repository, Tutorial
https://timmonko.github.io/napari-ndev/tutorial/01_example_pipeline/
I2K 2024: clEsperanto - GPU-Accelerated Image Processing Library#
Stephane Rigaud, Robert Haase
Licensed BSD-3-CLAUSE
Course and material for the clEsperanto workshop presented at I2K 2024 @ Human Technopol (Milan, Italy). The workshop is an hands-on demo of the clesperanto project, focussing on how to use the library for users who want use GPU-acceleration for their Image Processing pipeline.
Tags: Clesperanto, Training, Bioimage Analysis, Notebooks, Workflow
Content type: Github Repository, Workshop, Tutorial, Notebook
I2K2024 workshop material - Lazy Parallel Processing and Visualization of Large Data with ImgLib2, BigDataViewer, the N5-API, and Spark#
Stephan Saalfeld, Tobias Pietzsch
Published None
Licensed APACHE-2.0
Tags: Training
Content type: Workshop, Notebook, Github Repository
I2K2024(virtual) - Bio-Image Analysis Code Generation#
Robert Haase
Licensed BSD-3-CLAUSE
This repository contains training materials for the Tutorial “Bio-Image Analysis Code Generation” at the From Images To Knowledge (I2K) Conference (virtual) October 28th-30th 2024.
Tags: Bioimage Analysis, Notebooks, Biabob
Content type: Github Repository, Tutorial, Notebook
Lecture-materials of the DeepLife course#
Carl Herrmann, annavonbachmann, David Hoksza, Martin Schätz, Dario Malchiodi, jnguyenvan, Britta Velten, Elodie Laine, JanaBraunger, barwil
Published 2023-12-06
Licensed UNKNOWN
Tags: Bioinformatics
Content type: Github Repository, Slides, Notebook
Multiplexed tissue imaging - tools and approaches#
Agustín Andrés Corbat, OmFrederic, Jonas Windhager, Kristína Lidayová
Licensed CC-BY-4.0
Material for the I2K 2024 “Multiplexed tissue imaging - tools and approaches” workshop
Tags: Bioimage Analysis, Microscopy Image Analysis
Content type: Github Repository, Slides, Workshop
BIIFSweden/I2K2024-MTIWorkshop
https://docs.google.com/presentation/d/1R9-4lXAmTYuyFZpTMDR85SjnLsPZhVZ8/edit#slide=id.p1
NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne-Hackathon-2023, GitHub repository)#
Mohamed Abdrabbou, Mehrnaz Babaki, Tom Boissonnet, Michele Bortolomeazzi, Eik Dahms, Vanessa Fuchs, A. F. 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, Peter Zentis
Licensed CC-BY-4.0
This repository documents the first NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon), where topics like ‘Interoperability’, ‘REMBI / Mapping’, and ‘Neuroglancer (OMERO / zarr)’ were explored through collaborative discussions and workflow sessions, culminating in reports that bridge NFDI4Bioimage to DataPLANT. Funded by various DFG initiatives, this event emphasized documentation and use cases, contributing preparatory work for future interoperability projects at the 2nd de.NBI BioHackathon in Bielefeld.
Tags: Research Data Management, FAIR-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Github Repository
NLP Course#
Yandex School of Data Analysis
Licensed MIT
YSDA course in Natural Language Processing
Tags: Natural Language Processing
Content type: Github Repository
NeubiasPasteur2023_AdvancedCellPose#
Gaelle Letort
Licensed BSD-3-CLAUSE
Tutorial for running CellPose advanced functions
Tags: Cellpose, Segmentation
Content type: Github Repository
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
Object Tracking and Track Analysis using TrackMate and CellTracksColab#
Joanna Pylvänäinen
Published None
Licensed GPL-3.0
I2K 2024 workshop materials for “Object Tracking and Track Analysis using TrackMate and CellTracksColab”
Tags: Bioimage Analysis, Training
Content type: Github Repository, Tutorial, Workshop, Slides
Omero-tools#
Johannes Soltwedel
Licensed CC-BY-4.0
This repository contains a collection of tools for working with OMERO. Such tools can be working with the OMERO command line interface to transfer datasets between repositories, etc.
Tags: OMERO, Bioimage Analysis
Content type: Github Repository
Plugin “omero-batch-plugin”#
Licensed GPL-2.0
An ImageJ plugin to run a script or macro on a batch of images from/to OMERO.
Tags: OMERO, Imagej, Imagej Macro, Github
Content type: Github Repository
Plugin “omero-cli-transfer”#
Erick Martins Ratamero, Jean-Marie Burel, Will Moore, Guillaume Gay, Christoph Moehl, et al.
Published 2024-09-14
Licensed GPL-2.0
An OMERO CLI plugin for creating and using transfer packets between OMERO servers.
Tags: OMERO
Content type: Github Repository
Plugin “simple-omero-client”#
Pierre Pouchin, Rdornier, kekunn, Jean-Marie Burel
Licensed GPL-2.0
A wrapper library which can be called from scripts in Fiji, but can mostly be used in Maven projects to wrap calls to the underlying OMERO Java Gateway.
Tags: OMERO, Github, Fiji
Content type: Github Repository
Prompt-Engineering-LLMs-Course#
Published 2024-09-11T07:45:30+00:00
Licensed MIT
Tags: Llms, Prompt Engineering, Code Generation
Content type: Github Repository, Tutorial
HelmholtzAI-Consultants-Munich/Prompt-Engineering-LLMs-Course
QuPath for Python programmers#
Alan O’Callaghan, Léo Leplat
Published 2024-10-23
Licensed UNKNOWN
These are the notebooks and associated files for the i2k 2024 QuPath for Python programmers workshop.
Tags: Python, Notebooks, Open Source Software, Bioimage Analysis
Content type: Github Repository, Notebook, Collection
RDM_system_connector#
SaibotMagd
Licensed UNKNOWN
This tool is intended to link different research data management platforms with each other.
Tags: Research Data Management, Image Data Management
Content type: Github Repository
Scipy Cookbook#
Pauli Virtanen et al.
Licensed BSD-3-CLAUSE
This is a conversion and second life of SciPy Cookbook as a bunch of Ipython notebooks.
Tags: Bioimage Analysis
Content type: Github Repository
SimpleITK-Notebooks#
Ziv Yaniv et al.
Licensed APACHE-2.0 LICENSE
Jupyter notebooks for learning how to use SimpleITK
Tags: Bioimage Analysis, Simpleitk
Content type: Github Repository
Ultrack I2K 2024 Workshop Materials#
Jordão Bragantini, Teun Huijben
Licensed BSD3-CLAUSE
Tags: Segmentation, Bioimage Analysis, Training
Content type: Workshop, Github Repository, Tutorial
Virtual-I2K-2024-multiview-stitcher#
Published 2024-10-30T07:38:11+00:00
Licensed BSD-3-CLAUSE
Repository accompanying the multiview-stitcher tutorial for Virtual I2K 2024
Tags: Big Data, Bioimageanalysis
Content type: Github Repository, Tutorial
YMIA - Python-Based Event Series Training Material#
Riccardo Massei, Robert Haase, ENicolay
Published None
Licensed MIT
This repository offer access to teaching material and useful resources for the YMIA - Python-Based Event Series.
Tags: Python, Large Language Models, Prompt Engineering, Biabob, Bioimage Analysis, Microscopy Image Analysis
Content type: Github Repository, Slides
bioformats2raw Converter#
Melissa Linkert, Chris Allan, Josh Moore, Sébastien Besson, David Gault, et al.
Licensed GPL-2.0
Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.
Tags: Open Source Software, Bioimage Data
Content type: Application, Github Repository
i2k-2020-s3-zarr-workshop#
Constantin Pape, Christian Tischer
Licensed UNKNOWN
Tags: Python, Big Data
Content type: Github Repository
introduction-to-generative-ai#
Bruna Piereck, Alexander Botzki
Published 2024-09-27T14:38:51+00:00
Licensed CC-BY-4.0
Course repository for Strategic Use of Generative AI
Tags: Artificial Intelligence
Content type: Github Repository, Tutorial
nextflow-workshop#
Tuur Muyldermans, Kris Davie, Alexander, Nicolas Vannieuwkerke, Kobe Lavaerts, Marcel Ribeiro-Dantas, Bruna Piereck, Steff Taelman
Published 2023-03-29T10:40:04+00:00
Licensed CC-BY-4.0
Nextflow workshop materials March 2023
Tags: Workflow, Nextflow
Content type: Github Repository, Tutorial
ome-ngff-validator#
Will Moore, Josh Moore, Yaroslav Halchenko, Sébastien Besson
Published 2022-09-29
Licensed BSD-2-CLAUSE
Web page for validating OME-NGFF files.
Tags: Bioimage Data
Content type: Github Repository, Application
raw2ometiff Converter#
Melissa Linkert, Chris Allan, Sébastien Besson, Josh Moore
Licensed GPL-2.0
Java application to convert a directory of tiles to an OME-TIFF pyramid. This is the second half of iSyntax/.mrxs => OME-TIFF conversion.
Tags: Open Source Software, Bioimage Data
Content type: Application, Github Repository
scikit-learn MOOC#
Loïc Estève et al.
Licensed CC-BY-4.0
Machine learning in Python with scikit-learn MOOC
Tags: Bioimage Analysis, Machine Learning
Content type: Github Repository
skimage-tutorials#
Juan Nunez-Iglesias et al.
Licensed CC0 1.0 UNIVERSAL
skimage-tutorials - a collection of tutorials for the scikit-image package.
Tags: Bioimage Analysis, Scikit-Image
Content type: Github Repository
training-resources#
Christian Tischer, Antonio Politi, Toby Hodges, maulakhan, grinic, bugraoezdemir, Tim-Oliver Buchholz, Elnaz Fazeli, Aliaksandr Halavatyi, Dominik Kutra, Stefania Marcotti, AnniekStok, Felix, jhennies, Severina Klaus, Martin Schorb, Nima Vakili, Sebastian Gonzalez Tirado, Stefan Helfrich, Yi Sun, Ziqiang Huang, Jan Eglinger, Constantin Pape, Joel Lüthi, Matt McCormick, Oane Gros
Published 2020-04-23T07:51:38+00:00
Licensed CC-BY-4.0
Resources for teaching/preparing to teach bioimage analysis
Tags: Bioimageanalysis, Neurobias
Content type: Github Repository