Recently added (10)#

BIOMERO - A scalable and extensible image analysis framework#

Torec T. Luik, Rodrigo Rosas-Bertolini, Eric A.J. Reits, Ron A. Hoebe, Przemek M. Krawczyk

Published None

Licensed CC-BY-4.0

The authors introduce BIOMERO (bioimage analysis in OMERO), a bridge connecting OMERO, a renowned bioimaging data management platform, FAIR workflows, and high-performance computing (HPC) environments.

Tags: OMERO, Workflow, Bioimage Analysis, Image Data Management

Content type: Publication

https://doi.org/10.1016/j.patter.2024.101024


Building FAIR image analysis pipelines for high-content-screening (HCS) data using Galaxy#

Riccardo Massei, Matthias Berndt, Beatriz Serrano-Solano, Wibke Busch, Stefan Scholz, Hannes Bohring, Jo Nyffeler, Luise Reger, Jan Bumberger, Lucille Lopez-Delisle

Published 2024-11-06

Licensed CC-BY-4.0

Imaging is crucial across various scientific disciplines, particularly in life sciences, where it plays a key role in studies ranging from single molecules to whole organisms. However, the complexity and sheer volume of image data, especially from high-content screening (HCS) experiments involving cell lines or other organisms, present significant challenges. Managing and analysing this data efficiently requires well-defined image processing tools and analysis pipelines that align with the FAIR principles—ensuring they are findable, accessible, interoperable, and reusable across different domains. In the frame of NFDI4BioImaging (the National Research Data Infrastructure focusing on bioimaging in Germany), we want to find viable solutions for storing, processing, analysing, and sharing HCS data. In particular, we want to develop solutions to make findable and machine-readable metadata using (semi)automatic analysis pipelines. In scientific research, such pipelines are crucial for maintaining data integrity, supporting reproducibility, and enabling interdisciplinary collaboration. These tools can be used by different users to retrieve images based on specific attributes as well as support quality control by identifying appropriate metadata. Galaxy, an open-source, web-based platform for data-intensive research, offers a solution by enabling the construction of reproducible pipelines for image analysis. By integrating popular analysis software like CellProfiler and connecting with cloud services such as OMERO and IDR, Galaxy facilitates the seamless access and management of image data. This capability is particularly valuable in bioimaging, where automated pipelines can streamline the handling of complex metadata, ensuring data integrity and fostering interdisciplinary collaboration. This approach not only increases the efficiency of HCS bioimaging but also contributes to the broader scientific community’s efforts to embrace FAIR principles, ultimately advancing scientific discovery and innovation. In the present study, we proposed an automated analysis pipeline for storing, processing, analysing, and sharing HCS bioimaging data. The (semi)automatic workflow was developed by taking as a case study a dataset of zebrafish larvae and cell lines images previously obtained from an automated imaging system generating data in an HCS fashion. In our workflows, images are automatically enriched with metadata (i.e. key-value pairs, tags, raw data, regions of interest) and uploaded to the UFZ-OME Remote Objects (OMERO) server using a novel OMERO tool suite developed with GALAXY. Workflows give the possibility to the user to intuitively fetch images from the local server and perform image analysis (i.e. annotation) or even more complex toxicological analyses (dose response modelling). Furthermore, we want to improve the FAIRness of the protocol by adding a direct upload link to the Image Data Resource (IDR) repository to automatically prepare the data for publication and sharing.

https://zenodo.org/records/14044640

https://doi.org/10.5281/zenodo.14044640

https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/


Forschungsdatenmanagement zukunftsfest gestalten – Impulse für die Strukturevaluation der Nationalen Forschungsdateninfrastruktur (NFDI)#

Steuerungsgremium Allianz-Schwerpunkt, Alexander von Humboldt Foundation, Deutsche Forschungsgemeinschaft, Fraunhofer Society, German Rectors’ Conference, Leibniz Association, German National Academy of Sciences Leopoldina, German Academic Exchange Service, Helmholtz Association of German Research Centres, Max Planck Society

Published 2024-11-04

Licensed CC-BY-4.0

Arbeitspapier des Steuerungsgremiums des Allianz-Schwerpunkts “Digitalität in der Wissenschaft”

https://zenodo.org/records/14032908

https://doi.org/10.5281/zenodo.14032908


Galaxy Training#

Published None

Licensed CC-BY-4.0

Collection of tutorials developed and maintained by the worldwide Galaxy community.

Tags: Bioimage Analysis, Data Analysis

Content type: Collection, Tutorial

https://training.galaxyproject.org/


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


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


Open Micoscropy Environment (OME) Youtube Channel#

Published None

Licensed CC-BY-4.0

OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data

Tags: Open Source Software, Microscopy Image Analysis, Bioimage Data

Content type: Video, Collection

https://www.youtube.com/@OpenMicroscopyEnvironment


Stackview sliceplot example data#

Robert Haase

Published 2024-11-03

Licensed CC-BY-4.0

This is a dataset of PNG images of Bio-Image Data Science teaching slides. The png_umap.yml file contains a list of all images and a dimensionality reduced embedding (Uniform Manifold Approximation Projection, UMAP) made using OpenAI’s text-embedding-ada-002 model. A notebook for visualizing this data is published here: haesleinhuepf/stackview

https://zenodo.org/records/14030307

https://doi.org/10.5281/zenodo.14030307


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