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

ScaDS/BIDS-lecture-2024


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

NL-BioImaging/biomero


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

juglab/EmbedSeg


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/

timmonko/napari-ndev


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

StRigaud/clesperanto_workshop_I2K24


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

https://saalfeldlab.github.io/i2k2024-lazy-workshop/

saalfeldlab/i2k2024-lazy-workshop


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

haesleinhuepf/i2k2024-ai-code-generation


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

deeplife4eu/Lecture-materials


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

https://zenodo.org/doi/10.5281/zenodo.10609770


NLP Course#

Yandex School of Data Analysis

Licensed MIT

YSDA course in Natural Language Processing

Tags: Natural Language Processing

Content type: Github Repository

yandexdataschool/nlp_course


NeubiasPasteur2023_AdvancedCellPose#

Gaelle Letort

Licensed BSD-3-CLAUSE

Tutorial for running CellPose advanced functions

Tags: Cellpose, Segmentation

Content type: Github Repository

gletort/NeubiasPasteur2023_AdvancedCellPose


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

rmassei/2024-jn-omero-pipeline


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

CellMigrationLab/I2K_2024


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

https://biapol.github.io/omero-tools/


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

GReD-Clermont/omero_batch-plugin


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

ome/omero-cli-transfer


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

GReD-Clermont/simple-omero-client


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

qupath/i2k-qupath-for-python-programmers


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

SaibotMagd/RDM_system_connector


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

scipy/scipy-cookbook


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

InsightSoftwareConsortium/SimpleITK-Notebooks


Ultrack I2K 2024 Workshop Materials#

Jordão Bragantini, Teun Huijben

Licensed BSD3-CLAUSE

Tags: Segmentation, Bioimage Analysis, Training

Content type: Workshop, Github Repository, Tutorial

royerlab/ultrack-i2k2024

https://royerlab.github.io/ultrack-i2k2024/


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

m-albert/Virtual-I2K-2024-multiview-stitcher


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

rmassei/ymia_python_event_series_material


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

glencoesoftware/bioformats2raw


i2k-2020-s3-zarr-workshop#

Constantin Pape, Christian Tischer

Licensed UNKNOWN

Tags: Python, Big Data

Content type: Github Repository

tischi/i2k-2020-s3-zarr-workshop


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

vibbits/introduction-to-generative-ai

https://liascript.github.io/course/?https://raw.githubusercontent.com/vibbits/introduction-to-generative-ai/refs/heads/main/README.md


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

vibbits/nextflow-workshop

https://liascript.github.io/course/?https://raw.githubusercontent.com/vibbits/nextflow-workshop/main/README.md#1


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

https://ome.github.io/ome-ngff-validator/

ome/ome-ngff-validator


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

glencoesoftware/raw2ometiff


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

INRIA/scikit-learn-mooc


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

scikit-image/skimage-tutorials


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

NEUBIAS/training-resources