deploy: 6fbdd0f

Author: haesleinhuepf

_sources/authors/david_barry.md

@@ -0,0 +1,75 @@
+# David barry (4)
+## ARRIVE 2.0 checklist for "Automated staging of zebrafish embryos using machine learning"
+
+David Barry
+
+Published 2022-10-14
+
+Licensed CC-BY-4.0
+
+
+
+ARRIVE 2.0 checklist for "Automated staging of zebrafish embryos using machine learning"
+
+[https://zenodo.org/records/7198533](https://zenodo.org/records/7198533)
+
+[https://doi.org/10.5281/zenodo.7198533](https://doi.org/10.5281/zenodo.7198533)
+
+
+---
+
+## Multi-dimensional Imaging and Analysis Workshop
+
+David Barry, Todd Fallesen
+
+Published 2024-09-24
+
+Licensed CC-BY-4.0
+
+
+
+[https://zenodo.org/records/13832613](https://zenodo.org/records/13832613)
+
+[https://doi.org/10.5281/zenodo.13832613](https://doi.org/10.5281/zenodo.13832613)
+
+
+---
+
+## Promoting Reproducibility in Biomedical Research
+
+David Barry
+
+Published 2025-10-17
+
+Licensed CC-BY-4.0
+
+
+
+Reproducibility is a cornerstone of robust biomedical research, yet challenges persist, particularly in the complex domains of AI and bioimage informatics/analysis. In this presentation, I discuss the critical need for enhanced reproducibility in image-based biological studies and detail some strategies implemented at the Francis Crick Institute. Our Image Analysis Group aims to empower researchers with the tools and knowledge to independently analyse their data, focusing on key pillars: training, standardization, informed interpretation and self-sufficiency. Through dedicated workshops, we have taught hundreds of researchers fundamental image analysis concepts, emphasizing the impact of image quality and appropriate quantification on data reliability. I will also showcase some practical examples of our work and the challenges associated with ensuring they can be used reproducibly by others. Finally, I will discuss our latest work on common pitfalls in image data interpretation, highlighting the importance of rigorous image quality control.
+
+[https://zenodo.org/records/17377255](https://zenodo.org/records/17377255)
+
+[https://doi.org/10.5281/zenodo.17377255](https://doi.org/10.5281/zenodo.17377255)
+
+
+---
+
+## Promoting Reproducibility in Biomedical Research through Image Analysis
+
+David Barry
+
+Published 2025-01-29
+
+Licensed CC-BY-SA-4.0
+
+
+
+Slides presented at Empowering Healthcare with Automated Analysis at London Metropolitan University on 29th January 2025
+
+[https://zenodo.org/records/14767945](https://zenodo.org/records/14767945)
+
+[https://doi.org/10.5281/zenodo.14767945](https://doi.org/10.5281/zenodo.14767945)
+
+
+---
+

_sources/content_types/collection.md

@@ -903,7 +903,7 @@ Content type: Collection, Video
 
 ## NFDI4BIOIMAGE - a consortium of the National Research Data Infrastructure
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Licensed UNKNOWN
 

_sources/domain/doi.org.md

@@ -1,4 +1,4 @@
-# Doi.org (406)
+# Doi.org (408)
 ## "Management of Microscopy Image Data: An overview of OMERO, BioImage Archive and Image Data Resource"  2025 @ Uni Leipzig
 
 Vellutini, Bruno C., Cuenca, Marina B., Abhijeet Krishna, Alicja Szałapak, Modes, Carl D., Pavel Tomančák
@@ -502,6 +502,25 @@ EU AI Act
 [https://doi.org/10.5281/zenodo.19246441](https://doi.org/10.5281/zenodo.19246441)
 
 
+---
+
+## ARRIVE 2.0 checklist for "Automated staging of zebrafish embryos using machine learning"
+
+David Barry
+
+Published 2022-10-14
+
+Licensed CC-BY-4.0
+
+
+
+ARRIVE 2.0 checklist for "Automated staging of zebrafish embryos using machine learning"
+
+[https://zenodo.org/records/7198533](https://zenodo.org/records/7198533)
+
+[https://doi.org/10.5281/zenodo.7198533](https://doi.org/10.5281/zenodo.7198533)
+
+
 ---
 
 ## Abdominal Imaging Window (AIW) for Intravital Imaging
@@ -5209,7 +5228,7 @@ We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Resea
 
 ## It's time to publish - where can bioimage data go? by Henning Falk
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Published 2026-02-26
 
@@ -6368,6 +6387,23 @@ Tags: Include In Dalia
 [https://doi.org/10.5281/zenodo.6554166](https://doi.org/10.5281/zenodo.6554166)
 
 
+---
+
+## Multi-dimensional Imaging and Analysis Workshop
+
+David Barry, Todd Fallesen
+
+Published 2024-09-24
+
+Licensed CC-BY-4.0
+
+
+
+[https://zenodo.org/records/13832613](https://zenodo.org/records/13832613)
+
+[https://doi.org/10.5281/zenodo.13832613](https://doi.org/10.5281/zenodo.13832613)
+
+
 ---
 
 ## Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV1
@@ -9670,17 +9706,15 @@ David Barry
 
 Published 2025-01-29
 
-Licensed CC-BY-4.0 INTERNATIONAL
-
+Licensed CC-BY-SA-4.0
 
 
-Slides presented at Empowering Healthcare with Automated Analysis at London Metropolitan University.
 
-Tags: Reproducibility, Image Analysis, Include In Dalia
+Slides presented at Empowering Healthcare with Automated Analysis at London Metropolitan University on 29th January 2025
 
-Content type: Slides
+[https://zenodo.org/records/14767945](https://zenodo.org/records/14767945)
 
-[https://doi.org/10.5281/zenodo.14767944](https://doi.org/10.5281/zenodo.14767944)
+[https://doi.org/10.5281/zenodo.14767945](https://doi.org/10.5281/zenodo.14767945)
 
 
 ---
@@ -10102,7 +10136,7 @@ We present our attempt to reproduce Figure 7 of the article Presynapses con
 
 ## Santa Cloud's Workshop by Henning Falk
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Published 2026-11-14
 
@@ -11534,7 +11568,7 @@ Licensed CC-BY-4.0
 
 ## The Beauty of Metadata by Henning Falk
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Published 2026-03-13
 

_sources/domain/zenodo.org.md

@@ -1,4 +1,4 @@
-# Zenodo.org (393)
+# Zenodo.org (396)
 ## "Management of Microscopy Image Data: An overview of OMERO, BioImage Archive and Image Data Resource"  2025 @ Uni Leipzig
 
 Vellutini, Bruno C., Cuenca, Marina B., Abhijeet Krishna, Alicja Szałapak, Modes, Carl D., Pavel Tomančák
@@ -428,6 +428,25 @@ EU AI Act
 [https://doi.org/10.5281/zenodo.19246441](https://doi.org/10.5281/zenodo.19246441)
 
 
+---
+
+## ARRIVE 2.0 checklist for "Automated staging of zebrafish embryos using machine learning"
+
+David Barry
+
+Published 2022-10-14
+
+Licensed CC-BY-4.0
+
+
+
+ARRIVE 2.0 checklist for "Automated staging of zebrafish embryos using machine learning"
+
+[https://zenodo.org/records/7198533](https://zenodo.org/records/7198533)
+
+[https://doi.org/10.5281/zenodo.7198533](https://doi.org/10.5281/zenodo.7198533)
+
+
 ---
 
 ## Abdominal Imaging Window (AIW) for Intravital Imaging
@@ -5034,7 +5053,7 @@ We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Resea
 
 ## It's time to publish - where can bioimage data go? by Henning Falk
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Published 2026-02-26
 
@@ -6159,6 +6178,23 @@ Tags: Include In Dalia
 [https://doi.org/10.5281/zenodo.6554166](https://doi.org/10.5281/zenodo.6554166)
 
 
+---
+
+## Multi-dimensional Imaging and Analysis Workshop
+
+David Barry, Todd Fallesen
+
+Published 2024-09-24
+
+Licensed CC-BY-4.0
+
+
+
+[https://zenodo.org/records/13832613](https://zenodo.org/records/13832613)
+
+[https://doi.org/10.5281/zenodo.13832613](https://doi.org/10.5281/zenodo.13832613)
+
+
 ---
 
 ## Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV1
@@ -9396,6 +9432,25 @@ Reproducibility is a cornerstone of robust biomedical research, yet challenges p
 [https://doi.org/10.5281/zenodo.17377255](https://doi.org/10.5281/zenodo.17377255)
 
 
+---
+
+## Promoting Reproducibility in Biomedical Research through Image Analysis
+
+David Barry
+
+Published 2025-01-29
+
+Licensed CC-BY-SA-4.0
+
+
+
+Slides presented at Empowering Healthcare with Automated Analysis at London Metropolitan University on 29th January 2025
+
+[https://zenodo.org/records/14767945](https://zenodo.org/records/14767945)
+
+[https://doi.org/10.5281/zenodo.14767945](https://doi.org/10.5281/zenodo.14767945)
+
+
 ---
 
 ## Prompt Engineering, Agentic Workflows and Multi-modal Large Language Models
@@ -9809,7 +9864,7 @@ We present our attempt to reproduce Figure 7 of the article Presynapses con
 
 ## Santa Cloud's Workshop by Henning Falk
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Published 2026-11-14
 
@@ -11217,7 +11272,7 @@ Licensed CC-BY-4.0
 
 ## The Beauty of Metadata by Henning Falk
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Published 2026-03-13
 

_sources/licenses/cc-by-4.0.md

@@ -1,4 +1,4 @@
-# Cc-by-4.0 (484)
+# Cc-by-4.0 (486)
 ## "Management of Microscopy Image Data: An overview of OMERO, BioImage Archive and Image Data Resource"  2025 @ Uni Leipzig
 
 Vellutini, Bruno C., Cuenca, Marina B., Abhijeet Krishna, Alicja Szałapak, Modes, Carl D., Pavel Tomančák
@@ -530,6 +530,25 @@ EU AI Act
 [https://doi.org/10.5281/zenodo.19246441](https://doi.org/10.5281/zenodo.19246441)
 
 
+---
+
+## ARRIVE 2.0 checklist for "Automated staging of zebrafish embryos using machine learning"
+
+David Barry
+
+Published 2022-10-14
+
+Licensed CC-BY-4.0
+
+
+
+ARRIVE 2.0 checklist for "Automated staging of zebrafish embryos using machine learning"
+
+[https://zenodo.org/records/7198533](https://zenodo.org/records/7198533)
+
+[https://doi.org/10.5281/zenodo.7198533](https://doi.org/10.5281/zenodo.7198533)
+
+
 ---
 
 ## Abdominal Imaging Window (AIW) for Intravital Imaging
@@ -5646,7 +5665,7 @@ We acknowledge funding by the Deutsche Forschungsgemeinschaft (DFG, German Resea
 
 ## It's time to publish - where can bioimage data go? by Henning Falk
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Published 2026-02-26
 
@@ -6880,6 +6899,23 @@ Tags: Include In Dalia
 [https://doi.org/10.5281/zenodo.6554166](https://doi.org/10.5281/zenodo.6554166)
 
 
+---
+
+## Multi-dimensional Imaging and Analysis Workshop
+
+David Barry, Todd Fallesen
+
+Published 2024-09-24
+
+Licensed CC-BY-4.0
+
+
+
+[https://zenodo.org/records/13832613](https://zenodo.org/records/13832613)
+
+[https://doi.org/10.5281/zenodo.13832613](https://doi.org/10.5281/zenodo.13832613)
+
+
 ---
 
 ## Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV1
@@ -10886,7 +10922,7 @@ We present our attempt to reproduce Figure 7 of the article Presynapses con
 
 ## Santa Cloud's Workshop by Henning Falk
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Published 2026-11-14
 
@@ -12410,7 +12446,7 @@ Licensed CC-BY-4.0
 
 ## The Beauty of Metadata by Henning Falk
 
-Nfdi4Bioimage
+NFDI4BIOIMAGE
 
 Published 2026-03-13