deploy: 8c2184d

_sources/blog/readme.md

@@ -28,6 +28,8 @@ By Robert Haase
 
 Introduction to version control using git for collaborative, reproducible script editing.
 
+Tags: NFDI4BioImage
+
 [https://focalplane.biologists.com/2021/09/04/collaborative-bio-image-analysis-script-editing-with-git/](https://focalplane.biologists.com/2021/09/04/collaborative-bio-image-analysis-script-editing-with-git/)
 
 ## Sharing Your Poster on Figshare: A Community Guide to How-To and Why
@@ -37,3 +39,33 @@ By Elisabeth Kugler
 
 [https://focalplane.biologists.com/2023/07/26/sharing-your-poster-on-figshare/](https://focalplane.biologists.com/2023/07/26/sharing-your-poster-on-figshare/)
 
+## Running Deep-Learning Scripts in the BiA-PoL Omero Server
+
+
+
+[https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html](https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html)
+
+## Browsing the Open Microscopy Image Data Resource with Python
+
+
+
+[https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html](https://biapol.github.io/blog/robert_haase/browsing_idr/readme.html)
+
+## Getting started with Mambaforge and Python
+
+
+
+[https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html](https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html)
+
+## Promoting Data Management at the Nikon Imaging Center and Cell Biology Microscopy Facility
+
+
+
+[https://datamanagement.hms.harvard.edu/news/promoting-data-management-nikon-imaging-center-and-cell-biology-microscopy-facility](https://datamanagement.hms.harvard.edu/news/promoting-data-management-nikon-imaging-center-and-cell-biology-microscopy-facility)
+
+## Data handling in large-scale electron microscopy
+
+
+
+[https://blog.delmic.com/data-handling-in-large-scale-electron-microscopy](https://blog.delmic.com/data-handling-in-large-scale-electron-microscopy)
+

_sources/collection/readme.md

@@ -25,6 +25,14 @@ List of OMERO Workshops
 
 [https://www.openmicroscopy.org/events/](https://www.openmicroscopy.org/events/)
 
+## NextFlow core
+
+
+
+nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow
+
+[https://nf-co.re/](https://nf-co.re/)
+
 ## RDM4Mic Presentations
 
 
@@ -172,6 +180,30 @@ licensed GPL-3.0
 
 [https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop](https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop)
 
+## Research Data Management Seminar - Slides
+
+
+
+[https://zenodo.org/record/6602101](https://zenodo.org/record/6602101)
+
+## A biologist’s guide to planning and performing quantitative bioimaging experiments
+
+
+
+[https://doi.org/10.1371/journal.pbio.3002167]https://doi.org/10.1371/journal.pbio.3002167)
+
+[https://www.bioimagingguide.org/]https://www.bioimagingguide.org/)
+
+## Annotated high-throughput microscopy image sets for validation
+
+
+
+Broad Bioimage Benchmark Collection (BBBC)
+
+[https://www.nature.com/articles/nmeth.2083]https://www.nature.com/articles/nmeth.2083)
+
+[https://bbbc.broadinstitute.org/]https://bbbc.broadinstitute.org/)
+
 ## NEUBIAS YouTube Channel
 
 

_sources/document/readme.md

@@ -1,4 +1,54 @@
 # document
+## BiaPy: Bioimage analysis pipelines in Python
+
+
+
+BiaPy is an open source Python library for building bioimage analysis pipelines, also called workflows.
+
+[https://biapy.readthedocs.io/](https://biapy.readthedocs.io/)
+
+## Galaxy Documentation
+
+
+
+Galaxy is an open source, web-based platform for data intensive biomedical research.
+
+Tags: workflow engine
+
+[https://usegalaxy.org/](https://usegalaxy.org/)
+
+## Fractal Documentation
+
+
+
+Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization.
+
+Tags: workflow engine
+
+[https://fractal-analytics-platform.github.io/](https://fractal-analytics-platform.github.io/)
+
+## Snakemake Documentation
+
+
+
+The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
+
+Tags: workflow engine
+
+[https://snakemake.readthedocs.io/en/stable/]https://snakemake.readthedocs.io/en/stable/)
+
+[https://academic.oup.com/bioinformatics/article/28/19/2520/290322]https://academic.oup.com/bioinformatics/article/28/19/2520/290322)
+
+## NextFlow documentation
+
+
+
+Nextflow enables scalable and reproducible scientific workflows using software containers.
+
+Tags: workflow engine
+
+[https://www.nextflow.io/](https://www.nextflow.io/)
+
 ## OMERO documentation
 
 
@@ -26,3 +76,9 @@ Single slide outlining the most important aspect for starting research data mana
 
 [https://zenodo.org/record/3490058](https://zenodo.org/record/3490058)
 
+## Lund Declaration on Maximising the Benefits of Research Data
+
+
+
+[https://www.regeringen.se/contentassets/55e7d8fbf6df4a54ac56942b98d94e4f/lund-declaration-on-maximising-the-benefits-of-research-data-pa-engelska.pdf](https://www.regeringen.se/contentassets/55e7d8fbf6df4a54ac56942b98d94e4f/lund-declaration-on-maximising-the-benefits-of-research-data-pa-engelska.pdf)
+

_sources/documentation/readme.md

@@ -1,4 +1,90 @@
 # documentation
+## JIPipe: visual batch processing for ImageJ
+
+
+
+JIPipe is an open-source visual programming language for easy-access pipeline development
+
+Tags: NFDI4BioImage,workflow engine
+
+[https://www.nature.com/articles/s41592-022-01744-4]https://www.nature.com/articles/s41592-022-01744-4)
+
+[https://jipipe.hki-jena.de/]https://jipipe.hki-jena.de/)
+
+## MiToBo - A Toolbox for Image Processing and Analysis
+
+
+
+The Microscope Image Analysis Toolbox is a toolbox with a collection of algorithms for processing and analyzing digital images.
+
+Tags: workflow engine
+
+[https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103]https://openresearchsoftware.metajnl.com/articles/10.5334/jors.103)
+
+[https://mitobo.informatik.uni-halle.de/]https://mitobo.informatik.uni-halle.de/)
+
+## BiaPy: Bioimage analysis pipelines in Python
+
+
+
+BiaPy is an open source Python library for building bioimage analysis pipelines, also called workflows.
+
+[https://biapy.readthedocs.io/](https://biapy.readthedocs.io/)
+
+## Galaxy Documentation
+
+
+
+Galaxy is an open source, web-based platform for data intensive biomedical research.
+
+Tags: workflow engine
+
+[https://usegalaxy.org/](https://usegalaxy.org/)
+
+## Fractal Documentation
+
+
+
+Fractal is a framework to process high-content imaging data at scale and prepare it for interactive visualization.
+
+Tags: workflow engine
+
+[https://fractal-analytics-platform.github.io/](https://fractal-analytics-platform.github.io/)
+
+## Snakemake Documentation
+
+
+
+The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
+
+Tags: workflow engine
+
+[https://snakemake.readthedocs.io/en/stable/]https://snakemake.readthedocs.io/en/stable/)
+
+[https://academic.oup.com/bioinformatics/article/28/19/2520/290322]https://academic.oup.com/bioinformatics/article/28/19/2520/290322)
+
+## ModularImageAnalysis (MIA): Assembly of modularisedimage and object analysis workflows in ImageJ
+
+
+
+ModularImageAnalysis is a Fiji plugin providing a modular framework for assembling image and object analysis workflows
+
+Tags: workflow engine
+
+[https://doi.org/10.1111/jmi.13227]https://doi.org/10.1111/jmi.13227)
+
+[https://mianalysis.github.io/]https://mianalysis.github.io/)
+
+## NextFlow documentation
+
+
+
+Nextflow enables scalable and reproducible scientific workflows using software containers.
+
+Tags: workflow engine
+
+[https://www.nextflow.io/](https://www.nextflow.io/)
+
 ## OME Documentation