Skip to content

Commit

Permalink
deploy: 1e68d67
Browse files Browse the repository at this point in the history
  • Loading branch information
haesleinhuepf committed May 24, 2024
1 parent f5896cf commit 91a8787
Show file tree
Hide file tree
Showing 62 changed files with 923 additions and 746 deletions.
17 changes: 16 additions & 1 deletion _sources/authors/susanne_kunis.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Susanne kunis (5)
# Susanne kunis (6)
## A Cloud-Optimized Storage for Interactive Access of Large Arrays

Josh Moore, Susanne Kunis
Expand All @@ -14,6 +14,21 @@ Content type: publication, conference abstract
[https://doi.org/10.52825/cordi.v1i.285](https://doi.org/10.52825/cordi.v1i.285)


---

## A practical guide to bioimaging research data management in core facilities

Christian Schmidt, Tom Boissonnet, Julia Dohle, Karen Bernhardt, Elisa Ferrando-May, Tobias Wernet, Roland Nitschke, Susanne Kunis, Stefanie Weidtkamp-Peters



Tags: research data management

Content type: publication

[https://onlinelibrary.wiley.com/doi/10.1111/jmi.13317](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13317)


---

## MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community
Expand Down
17 changes: 16 additions & 1 deletion _sources/content_types/publication.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Publication (39)
# Publication (40)
## 2020 BioImage Analysis Survey: Community experiences and needs for the future

Nasim Jamali, Ellen T. A. Dobson, Kevin W. Eliceiri, Anne E. Carpenter, Beth A. Cimini
Expand Down Expand Up @@ -86,6 +86,21 @@ Content type: publication
[https://www.nature.com/articles/s41592-018-0195-8](https://www.nature.com/articles/s41592-018-0195-8)


---

## A practical guide to bioimaging research data management in core facilities

Christian Schmidt, Tom Boissonnet, Julia Dohle, Karen Bernhardt, Elisa Ferrando-May, Tobias Wernet, Roland Nitschke, Susanne Kunis, Stefanie Weidtkamp-Peters



Tags: research data management

Content type: publication

[https://onlinelibrary.wiley.com/doi/10.1111/jmi.13317](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13317)


---

## A study on long-term reproducibility of image analysis results on ImageJ and Fiji
Expand Down
21 changes: 20 additions & 1 deletion _sources/licenses/unknown.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Unknown (58)
# Unknown (59)
## 2022 MIC Workshop on Bioimage processing with Python

Guillaume Witz
Expand Down Expand Up @@ -333,6 +333,25 @@ Content type: book
[https://cytomining.github.io/DeepProfiler-handbook/docs/00-welcome.html](https://cytomining.github.io/DeepProfiler-handbook/docs/00-welcome.html)


---

## Diffusion Models for Image Restoration - An Introduction

Anirban Ray

Licensed unknown



Presentation given at the EMBO-DL4MIA 2024, Advanced Topic Seminar, May-11-2024

Tags: bioimage analysis, diffusion models, TU DRESDEN

Content type: presentation

[https://drive.google.com/file/d/1pPVUUMi5w2Ojw_SaBzSQVaXUuIKtQ7Ma/view](https://drive.google.com/file/d/1pPVUUMi5w2Ojw_SaBzSQVaXUuIKtQ7Ma/view)


---

## EMBL Deep Learning course 2019 exercises and materials
Expand Down
2 changes: 1 addition & 1 deletion _sources/readme.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# NFDI4BioImage Training Materials

This Jupyter Book contains 251 links to training materials in the context Research Data Management for Bioimaging / Microscopy Data and Bio-image Analysis and has been updated 2024-05-23.
This Jupyter Book contains 253 links to training materials in the context Research Data Management for Bioimaging / Microscopy Data and Bio-image Analysis and has been updated 2024-05-24.

This is a **preliminary** / **experimental** search index allowing us to explore how such a database could look like. We follow the principle [_release early, release often_](https://en.wikipedia.org/wiki/Release_early,_release_often) and aim at having a functional prototype of the search index at any time. We will use this resource to
* explore what kind of meta-data we need to collect for training materials
Expand Down
21 changes: 20 additions & 1 deletion _sources/tags/bioimage_analysis.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Bioimage analysis (107)
# Bioimage analysis (108)
## 2020 BioImage Analysis Survey: Community experiences and needs for the future

Nasim Jamali, Ellen T. A. Dobson, Kevin W. Eliceiri, Anne E. Carpenter, Beth A. Cimini
Expand Down Expand Up @@ -682,6 +682,25 @@ Content type: book
[https://cytomining.github.io/DeepProfiler-handbook/docs/00-welcome.html](https://cytomining.github.io/DeepProfiler-handbook/docs/00-welcome.html)


---

## Diffusion Models for Image Restoration - An Introduction

Anirban Ray

Licensed unknown



Presentation given at the EMBO-DL4MIA 2024, Advanced Topic Seminar, May-11-2024

Tags: bioimage analysis, diffusion models, TU DRESDEN

Content type: presentation

[https://drive.google.com/file/d/1pPVUUMi5w2Ojw_SaBzSQVaXUuIKtQ7Ma/view](https://drive.google.com/file/d/1pPVUUMi5w2Ojw_SaBzSQVaXUuIKtQ7Ma/view)


---

## EMBO Practical Course Advanced methods in bioimage analysis
Expand Down
17 changes: 16 additions & 1 deletion _sources/tags/research_data_management.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Research data management (46)
# Research data management (47)
## A Cloud-Optimized Storage for Interactive Access of Large Arrays

Josh Moore, Susanne Kunis
Expand Down Expand Up @@ -29,6 +29,21 @@ Content type: publication
[https://www.nature.com/articles/s41592-018-0195-8](https://www.nature.com/articles/s41592-018-0195-8)


---

## A practical guide to bioimaging research data management in core facilities

Christian Schmidt, Tom Boissonnet, Julia Dohle, Karen Bernhardt, Elisa Ferrando-May, Tobias Wernet, Roland Nitschke, Susanne Kunis, Stefanie Weidtkamp-Peters



Tags: research data management

Content type: publication

[https://onlinelibrary.wiley.com/doi/10.1111/jmi.13317](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13317)


---

## BigDataProcessor2: A free and open-source Fiji plugin for inspection and processing of TB sized image data
Expand Down
26 changes: 13 additions & 13 deletions authors/christian_tischer.html
Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../tags/bioimage_analysis.html">
Bioimage analysis (107)
Bioimage analysis (108)
</a>
</li>

Expand Down Expand Up @@ -225,7 +225,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../tags/research_data_management.html">
Research data management (46)
Research data management (47)
</a>
</li>

Expand Down Expand Up @@ -309,7 +309,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../content_types/publication.html">
Publication (39)
Publication (40)
</a>
</li>

Expand Down Expand Up @@ -386,7 +386,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../licenses/unknown.html">
Unknown (58)
Unknown (59)
</a>
</li>

Expand Down Expand Up @@ -493,7 +493,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../tags/bioimage_analysis.html">
Bioimage analysis (107)
Bioimage analysis (108)
</a>
</li>

Expand Down Expand Up @@ -561,7 +561,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../tags/research_data_management.html">
Research data management (46)
Research data management (47)
</a>
</li>

Expand Down Expand Up @@ -645,7 +645,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../content_types/publication.html">
Publication (39)
Publication (40)
</a>
</li>

Expand Down Expand Up @@ -722,7 +722,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../licenses/unknown.html">
Unknown (58)
Unknown (59)
</a>
</li>

Expand Down Expand Up @@ -813,7 +813,7 @@
<p aria-level="2" class="caption" role="heading"><span class="caption-text">By tag</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../tags/artificial_intelligence.html">Artificial intelligence (26)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/bioimage_analysis.html">Bioimage analysis (107)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/bioimage_analysis.html">Bioimage analysis (108)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/deep_learning.html">Deep learning (6)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/imagej.html">Imagej (16)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/meta_data.html">Meta data (6)</a></li>
Expand All @@ -822,7 +822,7 @@
<li class="toctree-l1"><a class="reference internal" href="../tags/nfdi4bioimage.html">Nfdi4bioimage (13)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/omero.html">Omero (16)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/python.html">Python (61)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/research_data_management.html">Research data management (46)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/research_data_management.html">Research data management (47)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/sharing.html">Sharing (7)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/workflow_engine.html">Workflow engine (12)</a></li>
</ul>
Expand All @@ -837,7 +837,7 @@
<li class="toctree-l1"><a class="reference internal" href="../content_types/documentation.html">Documentation (14)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/event.html">Event (7)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/notebook.html">Notebook (47)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/publication.html">Publication (39)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/publication.html">Publication (40)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/slide.html">Slide (39)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/slides.html">Slides (12)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/tutorial.html">Tutorial (14)</a></li>
Expand All @@ -851,7 +851,7 @@
<li class="toctree-l1"><a class="reference internal" href="../licenses/cc-by_4.0.html">Cc-by 4.0 (6)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../licenses/cc-by-4.0.html">Cc-by-4.0 (58)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../licenses/mit.html">Mit (13)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../licenses/unknown.html">Unknown (58)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../licenses/unknown.html">Unknown (59)</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Appendix</span></p>
<ul class="nav bd-sidenav">
Expand Down Expand Up @@ -1303,7 +1303,7 @@ <h2>i2k-2020-s3-zarr-workshop<a class="headerlink" href="#i2k-2020-s3-zarr-works

<div class="footer-item">
<p class="last-updated">
Last updated on 2024-05-23.<br>
Last updated on 2024-05-24.<br>
</p>
</div>

Expand Down
26 changes: 13 additions & 13 deletions authors/constantin_pape.html
Original file line number Diff line number Diff line change
Expand Up @@ -157,7 +157,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../tags/bioimage_analysis.html">
Bioimage analysis (107)
Bioimage analysis (108)
</a>
</li>

Expand Down Expand Up @@ -225,7 +225,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../tags/research_data_management.html">
Research data management (46)
Research data management (47)
</a>
</li>

Expand Down Expand Up @@ -309,7 +309,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../content_types/publication.html">
Publication (39)
Publication (40)
</a>
</li>

Expand Down Expand Up @@ -386,7 +386,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../licenses/unknown.html">
Unknown (58)
Unknown (59)
</a>
</li>

Expand Down Expand Up @@ -493,7 +493,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../tags/bioimage_analysis.html">
Bioimage analysis (107)
Bioimage analysis (108)
</a>
</li>

Expand Down Expand Up @@ -561,7 +561,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../tags/research_data_management.html">
Research data management (46)
Research data management (47)
</a>
</li>

Expand Down Expand Up @@ -645,7 +645,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../content_types/publication.html">
Publication (39)
Publication (40)
</a>
</li>

Expand Down Expand Up @@ -722,7 +722,7 @@

<li class="nav-item">
<a class="nav-link nav-internal" href="../licenses/unknown.html">
Unknown (58)
Unknown (59)
</a>
</li>

Expand Down Expand Up @@ -813,7 +813,7 @@
<p aria-level="2" class="caption" role="heading"><span class="caption-text">By tag</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="../tags/artificial_intelligence.html">Artificial intelligence (26)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/bioimage_analysis.html">Bioimage analysis (107)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/bioimage_analysis.html">Bioimage analysis (108)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/deep_learning.html">Deep learning (6)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/imagej.html">Imagej (16)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/meta_data.html">Meta data (6)</a></li>
Expand All @@ -822,7 +822,7 @@
<li class="toctree-l1"><a class="reference internal" href="../tags/nfdi4bioimage.html">Nfdi4bioimage (13)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/omero.html">Omero (16)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/python.html">Python (61)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/research_data_management.html">Research data management (46)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/research_data_management.html">Research data management (47)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/sharing.html">Sharing (7)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tags/workflow_engine.html">Workflow engine (12)</a></li>
</ul>
Expand All @@ -837,7 +837,7 @@
<li class="toctree-l1"><a class="reference internal" href="../content_types/documentation.html">Documentation (14)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/event.html">Event (7)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/notebook.html">Notebook (47)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/publication.html">Publication (39)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/publication.html">Publication (40)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/slide.html">Slide (39)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/slides.html">Slides (12)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../content_types/tutorial.html">Tutorial (14)</a></li>
Expand All @@ -851,7 +851,7 @@
<li class="toctree-l1"><a class="reference internal" href="../licenses/cc-by_4.0.html">Cc-by 4.0 (6)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../licenses/cc-by-4.0.html">Cc-by-4.0 (58)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../licenses/mit.html">Mit (13)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../licenses/unknown.html">Unknown (58)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../licenses/unknown.html">Unknown (59)</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Appendix</span></p>
<ul class="nav bd-sidenav">
Expand Down Expand Up @@ -1206,7 +1206,7 @@ <h2>i2k-2020-s3-zarr-workshop<a class="headerlink" href="#i2k-2020-s3-zarr-works

<div class="footer-item">
<p class="last-updated">
Last updated on 2024-05-23.<br>
Last updated on 2024-05-24.<br>
</p>
</div>

Expand Down
Loading

0 comments on commit 91a8787

Please sign in to comment.