deploy: 21e20d6

_sources/authors/beatriz_serrano-solano.md

@@ -90,7 +90,7 @@ Licensed UNKNOWN
 
 Tags: Bioimage Analysis
 
-Content type: Slide
+Content type: Slides
 
 [https://docs.google.com/presentation/d/1WG_4307XmKsGfWT3taxMvX2rZiG1k0SM1E7SAENJQkI/edit#slide=id.p](https://docs.google.com/presentation/d/1WG_4307XmKsGfWT3taxMvX2rZiG1k0SM1E7SAENJQkI/edit#slide=id.p)
 

_sources/authors/chris_allan.md

@@ -9,9 +9,9 @@ Licensed UNKNOWN
 
 Example Workflows / usage of the Glencoe Software.
 
-Tags: OMERO, Training
+Tags: OMERO
 
-Content type: Videos, Tutorial, Collection
+Content type: Video, Tutorial, Collection
 
 [https://www.glencoesoftware.com/media/webinars/](https://www.glencoesoftware.com/media/webinars/)
 
@@ -47,7 +47,7 @@ Licensed CC-BY-4.0
 
 The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results.
 
-Tags: Microscopy Image Analysis, Bioimage Analysis
+Tags: Bioimage Analysis
 
 Content type: Publication
 
@@ -68,7 +68,7 @@ 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
+Tags: Open Source Software
 
 Content type: Application, Github Repository
 
@@ -87,7 +87,7 @@ 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
+Tags: Open Source Software
 
 Content type: Application, Github Repository
 

_sources/authors/christian_schmidt.md

@@ -17,6 +17,8 @@ Research data management is essential in nowadays research, and one of the big o
 
 In this presentation, Stefanie Weidtkamp-Peters will introduce the challenges for bioimaging data management, and the necessary steps to achieve data FAIRification. German BioImaging - GMB e.V., together with other institutions, contributes to this endeavor. Janina Hanne will present how the network of imaging core facilities, research groups and industry partners is key to the German bioimaging community’s aligned collaboration toward FAIR bioimaging data. These activities have paved the way for two data management initiatives in Germany: I3D:bio (Information Infrastructure for BioImage Data) and NFDI4BIOIMAGE, a consortium of the National Research Data Infrastructure. Christian Schmidt will introduce the goals and measures of these initiatives to the benefit of imaging scientist’s work and everyday practice.  
 
+Tags: Nfdi4Bioimage, Research Data Management
+
 [https://zenodo.org/records/7890311](https://zenodo.org/records/7890311)
 
 [https://doi.org/10.5281/zenodo.7890311](https://doi.org/10.5281/zenodo.7890311)
@@ -70,7 +72,7 @@ Licensed UNKNOWN
 
 A Microscopy Research Data Management Resource.
 
-Tags: Metadata, I3Dbio, Research Data Management, Bioimage Data
+Tags: Metadata, I3Dbio, Research Data Management
 
 Content type: Collection
 
@@ -93,7 +95,7 @@ The open-source software OME Remote Objects (OMERO) is a data management softwar
 
 Tags: OMERO, Research Data Management, Nfdi4Bioimage, I3Dbio
 
-Content type: Slide, Video
+Content type: Slides, Video
 
 [https://zenodo.org/records/8323588](https://zenodo.org/records/8323588)
 
@@ -132,6 +134,8 @@ See cross reference:
 10.5281/zenodo.12547566 Key-Value pair template for annotation of datasets in OMERO (light- and electron microscopy data within the research group of Prof. Mueller-Reichert)
 10.5281/zenodo.12578084 Key-Value pair template for annotation in OMERO for light microscopy data acquired with AxioScan7 - Core Facility Cellular Imaging (CFCI)
 
+Tags: Nfdi4Bioimage, Research Data Management
+
 [https://zenodo.org/records/12546808](https://zenodo.org/records/12546808)
 
 [https://doi.org/10.5281/zenodo.12546808](https://doi.org/10.5281/zenodo.12546808)
@@ -206,9 +210,9 @@ Licensed CCY-BY-SA-4.0
 
 Align existing and establish novel services & solutions for data management tasks throughout the bioimage data lifecycle.
 
-Tags: Nfdi4Bioimage, Image Data Management, Bioimage Data, Research Data Management
+Tags: Nfdi4Bioimage, Research Data Management
 
-Content type: Conference Abstract, Slide
+Content type: Conference Abstract, Slides
 
 [https://doi.org/10.11588/heidok.00029489](https://doi.org/10.11588/heidok.00029489)
 
@@ -227,7 +231,7 @@ Licensed CC-BY-4.0
 
 As an initiative within Germany's National Research Data Infrastructure, the authors conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs.
 
-Tags: Research Data Management, Image Data Management, Bioimage Data
+Tags: Research Data Management
 
 Content type: Publication
 
@@ -265,6 +269,8 @@ Licensed CC-BY-4.0
 
 Research data management (RDM) in microscopy and image analysis is a challenging task. Large files in proprietary formats, complex N-dimensional array structures, and various metadata models and formats can make image data handling inconvenient and difficult. For data organization, annotation, and sharing, researchers need solutions that fit everyday practice and comply with the FAIR (Findable, Accessible, Interoperable, Reusable) principles. International community-based efforts have begun creating open data models (OME), an open file format and translation library (OME-TIFF, Bio-Formats), data management software platforms, and microscopy metadata recommendations and annotation tools. Bringing these developments into practice requires support and training. Iterative feedback and tool improvement is needed to foster practical adoption by the scientific community. The Information Infrastructure for BioImage Data (I3D:bio) project works on guidelines, training resources, and practical assistance for FAIR microscopy RDM adoption with a focus on the management platform OMERO and metadata annotations.
 
+Tags: Nfdi4Bioimage, Research Data Management
+
 [https://zenodo.org/records/10805204](https://zenodo.org/records/10805204)
 
 [https://doi.org/10.5281/zenodo.10805204](https://doi.org/10.5281/zenodo.10805204)
@@ -284,6 +290,8 @@ Licensed CC-BY-4.0
 
 Germany’s National Research Data Infrastructure (NFDI) aims to establish a sustained, cross-disciplinary research data management (RDM) infrastructure that enables researchers to handle FAIR (findable, accessible, interoperable, reusable) data. While FAIR principles have been adopted by funders, policymakers, and publishers, their practical implementation remains an ongoing effort. In the field of bio-imaging, harmonization of data formats, metadata ontologies, and open data repositories is necessary to achieve FAIR data. The NFDI4BIOIMAGE was established to address these issues and develop tools and best practices to facilitate FAIR microscopy and image analysis data in alignment with international community activities. The consortium operates through its Data Stewards team to provide expertise and direct support to help overcome RDM challenges. The three Helmholtz Centers in NFDI4BIOIMAGE aim to collaborate closely with other centers and initiatives, such as HMC, Helmholtz AI, and HIP. Here we present NFDI4BIOIMAGE’s work and its significance for research in Helmholtz and beyond
 
+Tags: Nfdi4Bioimage, Research Data Management
+
 [https://zenodo.org/records/11501662](https://zenodo.org/records/11501662)
 
 [https://doi.org/10.5281/zenodo.11501662](https://doi.org/10.5281/zenodo.11501662)
@@ -370,6 +378,8 @@ Learn from each other, leverage different expertise
 Learn how to train users, establish sustainability strategies, and foster FAIR RDM for bioimaging at your institution
 
 
+Tags: Nfdi4Bioimage, Research Data Management
+
 [https://zenodo.org/records/14178789](https://zenodo.org/records/14178789)
 
 [https://doi.org/10.5281/zenodo.14178789](https://doi.org/10.5281/zenodo.14178789)
@@ -401,6 +411,8 @@ Dr. Riccardo Massei (Helmholtz-Center for Environmental Research, UFZ, Leipzig)
 Dr. Michele Bortolomeazzi (DKFZ, Single cell Open Lab, bioimage data specialist, bioinformatician, staff scientist in the NFDI4BIOIMAGE project)
 Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg, Project Coordinator of the NFDI4BIOIMAGE project)
 
+Tags: Nfdi4Bioimage, Research Data Management
+
 [https://zenodo.org/records/11350689](https://zenodo.org/records/11350689)
 
 [https://doi.org/10.5281/zenodo.11350689](https://doi.org/10.5281/zenodo.11350689)
@@ -484,6 +496,8 @@ Publishing datasets in public archives for bioimage dataKsenia Krooß /Hein
 
 Date & Venue:Thursday, Sept. 26, 5.30 p.m.Haus 22 / Paul Ehrlich Lecture Hall (H22-1)University Hospital Frankfurt
 
+Tags: Nfdi4Bioimage, Research Data Management
+
 [https://zenodo.org/records/13861026](https://zenodo.org/records/13861026)
 
 [https://doi.org/10.5281/zenodo.13861026](https://doi.org/10.5281/zenodo.13861026)

_sources/authors/christian_tischer.md

@@ -60,7 +60,7 @@ Licensed UNKNOWN
 
 
 
-Content type: Slide
+Content type: Slides
 
 [https://github.com/tischi/presentation-image-analysis](https://github.com/tischi/presentation-image-analysis)
 
@@ -126,7 +126,7 @@ Licensed CC-BY-4.0
 
 Tags: Bioimage Analysis
 
-Content type: Online Tutorial, Video, Slide
+Content type: Online Tutorial, Video, Slides
 
 [https://www.ebi.ac.uk/training/events/methods-bioimage-analysis/](https://www.ebi.ac.uk/training/events/methods-bioimage-analysis/)
 
@@ -139,7 +139,7 @@ Content type: Online Tutorial, Video, Slide
 
 ## Modular training resources for bioimage analysis
 
-Christian Tischer, Antonio Politi, Tim-Oliver Buchholz, Elnaz Fazeli, Nicola Gritti, Aliaksandr Halavatyi, Gonzalez Tirado, Sebastian, Julian Hennies, Toby Hodges, Arif Khan, Dominik Kutra, Stefania Marcotti, Bugra Oezdemir, Felix Schneider, Martin Schorb, Anniek Stokkermans, Yi Sun, Nima Vakili
+Christian Tischer, Antonio Politi, Tim-Oliver Buchholz, Elnaz Fazeli, Nicola Gritti, Aliaksandr Halavatyi, Sebastian Gonzalez Tirado, Julian Hennies, Toby Hodges, Arif Khan, Dominik Kutra, Stefania Marcotti, Bugra Oezdemir, Felix Schneider, Martin Schorb, Anniek Stokkermans, Yi Sun, Nima Vakili
 
 Published 2024-12-03
 
@@ -149,6 +149,8 @@ Licensed CC-BY-4.0
 
 Resources for teaching/preparing to teach bioimage analysis
 
+Tags: Neubias, Bioimage Analysis
+
 [https://zenodo.org/records/14264885](https://zenodo.org/records/14264885)
 
 [https://doi.org/10.5281/zenodo.14264885](https://doi.org/10.5281/zenodo.14264885)

_sources/authors/constantin_pape.md

@@ -24,7 +24,7 @@ Licensed UNKNOWN
 
 Tags: Artificial Intelligence, Bioimage Analysis
 
-Content type: Slide, Notebook
+Content type: Slides, Notebook
 
 [https://github.com/JLrumberger/DL-MBL-2021](https://github.com/JLrumberger/DL-MBL-2021)
 
@@ -65,7 +65,7 @@ Overview of Segment Anythign for Microscopy given at the SWISSBIAS online meetin
 Talk about vision foundation models and Segment Anything for Microscopy given at Human Technopole as part of the EMBO Deep Learning Course in May 2024
 
 
-Tags: Image Segmentation, Bioimage Analysis, Deep Learning
+Tags: Bioimage Analysis, Artificial Intelligence
 
 Content type: Slides
 

_sources/authors/cornelia_wetzker.md

@@ -30,9 +30,9 @@ Licensed CC-BY-4.0
 
 This presentation gives a short outline of the complexity of data and metadata in the bioimaging universe. It introduces NFDI4BIOIMAGE as a newly formed consortium as part of the German 'Nationale Forschungsdateninfrastruktur' (NFDI) and its goals and tools for data management including its current members on TU Dresden campus.  
 
-Tags: Research Data Management, Tu Dresden, Bioimage Data, Nfdi4Bioimage
+Tags: Research Data Management, Nfdi4Bioimage
 
-Content type: Slide
+Content type: Slides
 
 [https://zenodo.org/records/10083555](https://zenodo.org/records/10083555)
 

_sources/authors/dominik_kutra.md

@@ -9,7 +9,7 @@ Licensed CC-BY-4.0
 
 This lesson shows how to use Python and scikit-image to do basic image processing.
 
-Tags: Segmentation, Bioimage Analysis, Training, Python, Scikit-Image, Image Segmentation
+Tags: Bioimage Analysis, Python
 
 Content type: Tutorial, Workflow
 
@@ -28,7 +28,7 @@ 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
+Tags: Bioimage Analysis, Python, Artificial Intelligence
 
 Content type: Video, Slides
 
@@ -39,7 +39,7 @@ Content type: Video, Slides
 
 ## Modular training resources for bioimage analysis
 
-Christian Tischer, Antonio Politi, Tim-Oliver Buchholz, Elnaz Fazeli, Nicola Gritti, Aliaksandr Halavatyi, Gonzalez Tirado, Sebastian, Julian Hennies, Toby Hodges, Arif Khan, Dominik Kutra, Stefania Marcotti, Bugra Oezdemir, Felix Schneider, Martin Schorb, Anniek Stokkermans, Yi Sun, Nima Vakili
+Christian Tischer, Antonio Politi, Tim-Oliver Buchholz, Elnaz Fazeli, Nicola Gritti, Aliaksandr Halavatyi, Sebastian Gonzalez Tirado, Julian Hennies, Toby Hodges, Arif Khan, Dominik Kutra, Stefania Marcotti, Bugra Oezdemir, Felix Schneider, Martin Schorb, Anniek Stokkermans, Yi Sun, Nima Vakili
 
 Published 2024-12-03
 
@@ -49,6 +49,8 @@ Licensed CC-BY-4.0
 
 Resources for teaching/preparing to teach bioimage analysis
 
+Tags: Neubias, Bioimage Analysis
+
 [https://zenodo.org/records/14264885](https://zenodo.org/records/14264885)
 
 [https://doi.org/10.5281/zenodo.14264885](https://doi.org/10.5281/zenodo.14264885)
@@ -85,7 +87,7 @@ Licensed CC-BY-4.0
 
 Tags: Artificial Intelligence, Bioimage Analysis
 
-Content type: Slide
+Content type: Slides
 
 [https://zenodo.org/doi/10.5281/zenodo.4330625](https://zenodo.org/doi/10.5281/zenodo.4330625)
 

_sources/authors/elisa_ferrando-may.md

@@ -28,7 +28,7 @@ The open-source software OME Remote Objects (OMERO) is a data management softwar
 
 Tags: OMERO, Research Data Management, Nfdi4Bioimage, I3Dbio
 
-Content type: Slide, Video
+Content type: Slides, Video
 
 [https://zenodo.org/records/8323588](https://zenodo.org/records/8323588)
 
@@ -51,9 +51,9 @@ Licensed CCY-BY-SA-4.0
 
 Align existing and establish novel services & solutions for data management tasks throughout the bioimage data lifecycle.
 
-Tags: Nfdi4Bioimage, Image Data Management, Bioimage Data, Research Data Management
+Tags: Nfdi4Bioimage, Research Data Management
 
-Content type: Conference Abstract, Slide
+Content type: Conference Abstract, Slides
 
 [https://doi.org/10.11588/heidok.00029489](https://doi.org/10.11588/heidok.00029489)
 
@@ -72,7 +72,7 @@ Licensed CC-BY-4.0
 
 As an initiative within Germany's National Research Data Infrastructure, the authors conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs.
 
-Tags: Research Data Management, Image Data Management, Bioimage Data
+Tags: Research Data Management
 
 Content type: Publication
 
@@ -110,6 +110,8 @@ Licensed CC-BY-4.0
 
 Research data management (RDM) in microscopy and image analysis is a challenging task. Large files in proprietary formats, complex N-dimensional array structures, and various metadata models and formats can make image data handling inconvenient and difficult. For data organization, annotation, and sharing, researchers need solutions that fit everyday practice and comply with the FAIR (Findable, Accessible, Interoperable, Reusable) principles. International community-based efforts have begun creating open data models (OME), an open file format and translation library (OME-TIFF, Bio-Formats), data management software platforms, and microscopy metadata recommendations and annotation tools. Bringing these developments into practice requires support and training. Iterative feedback and tool improvement is needed to foster practical adoption by the scientific community. The Information Infrastructure for BioImage Data (I3D:bio) project works on guidelines, training resources, and practical assistance for FAIR microscopy RDM adoption with a focus on the management platform OMERO and metadata annotations.
 
+Tags: Nfdi4Bioimage, Research Data Management
+
 [https://zenodo.org/records/10805204](https://zenodo.org/records/10805204)
 
 [https://doi.org/10.5281/zenodo.10805204](https://doi.org/10.5281/zenodo.10805204)
@@ -129,6 +131,8 @@ Licensed CC-BY-4.0
 
 Germany’s National Research Data Infrastructure (NFDI) aims to establish a sustained, cross-disciplinary research data management (RDM) infrastructure that enables researchers to handle FAIR (findable, accessible, interoperable, reusable) data. While FAIR principles have been adopted by funders, policymakers, and publishers, their practical implementation remains an ongoing effort. In the field of bio-imaging, harmonization of data formats, metadata ontologies, and open data repositories is necessary to achieve FAIR data. The NFDI4BIOIMAGE was established to address these issues and develop tools and best practices to facilitate FAIR microscopy and image analysis data in alignment with international community activities. The consortium operates through its Data Stewards team to provide expertise and direct support to help overcome RDM challenges. The three Helmholtz Centers in NFDI4BIOIMAGE aim to collaborate closely with other centers and initiatives, such as HMC, Helmholtz AI, and HIP. Here we present NFDI4BIOIMAGE’s work and its significance for research in Helmholtz and beyond
 
+Tags: Nfdi4Bioimage, Research Data Management
+
 [https://zenodo.org/records/11501662](https://zenodo.org/records/11501662)
 
 [https://doi.org/10.5281/zenodo.11501662](https://doi.org/10.5281/zenodo.11501662)

_sources/authors/elnaz_fazeli.md

@@ -39,7 +39,7 @@ Bioimaging has transformed our understanding of biological processes, yet extrac
 
 ## Modular training resources for bioimage analysis
 
-Christian Tischer, Antonio Politi, Tim-Oliver Buchholz, Elnaz Fazeli, Nicola Gritti, Aliaksandr Halavatyi, Gonzalez Tirado, Sebastian, Julian Hennies, Toby Hodges, Arif Khan, Dominik Kutra, Stefania Marcotti, Bugra Oezdemir, Felix Schneider, Martin Schorb, Anniek Stokkermans, Yi Sun, Nima Vakili
+Christian Tischer, Antonio Politi, Tim-Oliver Buchholz, Elnaz Fazeli, Nicola Gritti, Aliaksandr Halavatyi, Sebastian Gonzalez Tirado, Julian Hennies, Toby Hodges, Arif Khan, Dominik Kutra, Stefania Marcotti, Bugra Oezdemir, Felix Schneider, Martin Schorb, Anniek Stokkermans, Yi Sun, Nima Vakili
 
 Published 2024-12-03
 
@@ -49,6 +49,8 @@ Licensed CC-BY-4.0
 
 Resources for teaching/preparing to teach bioimage analysis
 
+Tags: Neubias, Bioimage Analysis
+
 [https://zenodo.org/records/14264885](https://zenodo.org/records/14264885)
 
 [https://doi.org/10.5281/zenodo.14264885](https://doi.org/10.5281/zenodo.14264885)

_sources/authors/estibaliz_gómez-de-mariscal.md

@@ -9,7 +9,7 @@ Licensed UNKNOWN
 
 Tags: Artificial Intelligence, Bioimage Analysis
 
-Content type: Slide
+Content type: Slides
 
 [https://github.com/esgomezm/NEUBIAS_chapter_DL_2020](https://github.com/esgomezm/NEUBIAS_chapter_DL_2020)
 
@@ -57,7 +57,7 @@ Licensed UNKNOWN
 
 Tags: Artificial Intelligence, Bioimage Analysis
 
-Content type: Slide
+Content type: Slides
 
 [https://raw.githubusercontent.com/esgomezm/esgomezm.github.io/master/assets/pdf/SPAOM2018/MachineLearning_SPAOMworkshop_public.pdf](https://raw.githubusercontent.com/esgomezm/esgomezm.github.io/master/assets/pdf/SPAOM2018/MachineLearning_SPAOMworkshop_public.pdf)
 
@@ -74,7 +74,7 @@ Licensed UNKNOWN
 
 Tags: Neubias, Bioimage Analysis
 
-Content type: Slide, Code, Notebook
+Content type: Slides, Code, Notebook
 
 [https://github.com/miura/NEUBIAS_AnalystSchool2020](https://github.com/miura/NEUBIAS_AnalystSchool2020)
 
@@ -91,7 +91,7 @@ Licensed UNKNOWN
 
 Tags: Artificial Intelligence, Bioimage Analysis
 
-Content type: Slide
+Content type: Slides
 
 [https://github.com/esgomezm/zidas2020_intro_DL](https://github.com/esgomezm/zidas2020_intro_DL)