Merge pull request #113 from NFDI4BIOIMAGE/fix-auto-update

auto-update

resources/blog_posts.yml

@@ -94,7 +94,6 @@ resources:
   - bioimage analysis
   type: blog
   url: https://focalplane.biologists.com/2023/03/02/rescaling-images-and-pixel-anisotropy/
-
 - authors: Jens Wendt
   name: User friendly Image metadata annotation tool/workflow for OMERO
   tags:

resources/events.yml

@@ -44,26 +44,141 @@ resources:
   - event
   - notebook
   url: https://biapol.github.io/PoL-BioImage-Analysis-TS-Early-Career-Track/intro.html
-- name: "FAIR data handling for microscopy: Structured metadata annotation in OMERO"
+- authors: Fuchs, Vanessa Aphaia Fiona, Schmidt, Christian, Boissonnet, Tom
+  description: 'Description
+
+    Microscopy experiments generate information-rich, multi-dimensional data, allowing
+    us to investigate biological processes at high spatial and temporal resolution.
+    Image processing and analysis is a standard procedure to retrieve quantitative
+    information from biological imaging. Due to the complex nature of bioimaging files
+    that often come in proprietary formats, it can be challenging to organize, structure,
+    and annotate bioimaging data throughout a project. Data often needs to be moved
+    between collaboration partners, transformed into open formats, processed with
+    a variety of software tools, and exported to smaller-sized images for presentation.
+    The path from image acquisition to final publication figures with quantitative
+    results must be documented and reproducible.
+
+    In this workshop, participants learn how to use structured metadata annotations
+    in the image data management platform OMERO (OME Remote Objects) to optimize their
+    data handling. This strategy helps both with organizing data for easier processing
+    and analysis and for the preparation of data publication in journal manuscripts
+    and in public repositories such as the BioImage Archive. Participants learn the
+    principles of leveraging object-oriented data organization in OMERO to enhance
+    findability and usability of their data, also in collaborative settings. The integration
+    of OMERO with image analysis tools, in particular ImageJ/Fiji, will be trained.
+    Moreover, users learn about community-accepted metadata checklists (REMBI) to
+    enrich the value of their data toward reproducibility and reusability. In this
+    workshop, we will provide hands-on training and recommendations on:
+
+
+    Structured metadata annotation features in OMERO and how to use them
+
+    Types of metadata in bioimaging: Technical metadata, sample metadata, analysis
+    metadata
+
+    The use of ontologies and terminologies for metadata annotation
+
+    REMBI, the recommended metadata for biological images
+
+    Metadata-assisted image analysis streamlining
+
+    Tools for metadata annotation in OMERO
+
+
+    The target group for this workshop
+
+    This workshop is directed at researchers at all career levels who have started
+    using OMERO for their microscopy research data management. We encourage the workshop
+    participants to bring example data from their research to discuss suitable metadata
+    annotation for their everyday practice.
+
+    Who are the trainers (see trainer description below for more details)
+
+
+    Dr. Vanessa Fuchs (NFDI4BIOIMAGE Data Steward, Center for Advanced Imaging, Heinrich-Heine
+    University of Düsseldorf)
+
+    Dr. Tom Boissonnet (OMERO admin and image metadata specialist, Center for Advanced
+    Imaging, Heinrich-Heine University of Düsseldorf)
+
+    Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging,
+    German Cancer Research Center, Heidelberg)
+
+
+    Material Description
+
+    Published here are the presentation slides that were used for input from the trainers
+    during the different sessions of the programme. Additionally, a Fiji Macro is
+    published that depends on the OMERO Extensions Plugin by Pouchin et al, 2022,
+    F100Research, https://doi.org/10.12688/f1000research.110385.2 
+
+    Programme Overview
+
+    Day 1 - April 29th, 2024 09.00 a.m. to 10.00 a.m.: Session 1 - Welcome and
+    Introduction
+
+    10.00 a.m. to 10.30 a.m.:  Session 2 - Introduction to the FAIR principles
+    & data annotation
+
+    10:30 a.m. to 10:45 a.m.: Coffee break
+
+    10.45 a.m. to 12.00 a.m.: Session 3 - Data structure (datasets in OMERO) and organization
+    with Tags 
+
+    12.00 a.m. to 1.00 p.m.:  Lunch Break
+
+    1.00 p.m. to 2.00 p.m.:  Session 4 - REMBI, Key-Value pair annotations in
+    bioimaging
+
+    2:00 p.m. to 2.30 p.m.:  Session 5 - Ontologies for Key-Value Pairs in OMERO
+
+    2:30 p.m. to 2:45 p.m. Coffee break
+
+    2.45 p.m. to 3.45 p.m.:  Wrap-up, discussion, outlook on day 2
+
+    Day 2 - April 30th, 2024
+
+    09.00 a.m. to 09.30 a.m.:  Arrival and Start into day 2
+
+    09.30 a.m. to 11.30 a.m.:  Session 6 - Hands-on : REMBI-based Key-Value Pair
+    annotation in OMERO
+
+    11.30 a.m. to 12.30 a.m.:  Lunch Break
+
+    12.30 a.m. to 1.15 p.m.: Session 7 - OMERO and OMERO.plugins
+
+    1.15 p.m. to 2.00 p.m.: Session 8 - Loading OMERO-hosted data into Fiji
+
+    2.00 p.m. to 2.15 p.m.: Coffee break 
+
+    2.15 p.m. to 3.00 p.m.: Discussion, Outlook'
+  license: cc-by-4.0
+  name: '[Workshop] FAIR data handling for microscopy: Structured metadata annotation
+    in OMERO'
+  num_downloads: 195
+  publication_date: '2024-05-06'
   tags:
   - research data management
   - omero
-  type: 
+  type:
   - workshop
   - slides
   - dataset
-  url: https://zenodo.org/records/11109616 
-- name: "Bring your own data workshops"
+  url:
+  - https://zenodo.org/records/11109616
+  - https://doi.org/10.5281/zenodo.11109616
+- name: Bring your own data workshops
   tags:
   - bioimage analysis
   - research data management
   type:
   - workshop
-  url: https://www.dtls.nl/fair-data/byod/ 
-- name: "Workshop-June2024-Madrid"
+  url: https://www.dtls.nl/fair-data/byod/
+- license: mit
+  name: Workshop-June2024-Madrid
   tags:
   - bioimage analysis
   type:
   - workshop
   - collection
-  url: https://github.com/bioimage-io/Workshop-June2024-Madrid 
+  url: https://github.com/bioimage-io/Workshop-June2024-Madrid