deploy: f80599b

Author: haesleinhuepf

_downloads/6de7f639209cca3eaecd5d9517493106/training_materials.csv

@@ -186,3 +186,8 @@ Python for Bioimage Analysis Basic Tools and Setup on Windows,Alberto Díez,http
 NFDITalk Cloud based image data science,"Josh Moore, Yi Sun",https://www.youtube.com/watch?v=bzfmE29S270,"Bioimage Analysis, OMERO, Exclude From Dalia",UNKNOWN,"In this talk, we will be discussing OME-ZARR, a cloud-optimized format for scalable bioimage data management, and BARD,  a cloud virtual desktop that provides a seamless way to run resource-intensive applications in the cloud, enabling users to access powerful computing environments from any device with a web browser."
 From Click to Code: Reproducibility in Bio-image Analysis,Mara Lampert,https://focalplane.biologists.com/2025/08/05/from-click-to-code-reproducibility-in-bio-image-analysis/,"Bioimage Analysis, Include In Dalia",CC-BY-4.0,"This blog post revolves around reproducibility in bio-image analysis  across several popular platforms, including Napari, Fiji, QuPath, Galaxy, CellProfiler and JIPipe."
 "Autopilot, Copilot, and Software Developers",Rahul Pandita,https://rahulpandita.me/blog/2025-10-12-Copilot,"Artificial Intelligence, Include In Dalia",UNKNOWN,"Language models (LLMs) are rapidly becoming essential developer tools. But the metaphors we use to describe them matter. One often used is: ""LLMs are the autopilot of coding."" As both a developer and a pilot, that metaphor misses the mark on several levels. This blog post pens down why ""Copilot"" is a far better analogy than ""autopilot"" when it comes to LLMs and vibe coding."
+RDM4mic Meeting 2025 Talks,"Cornelia Wetzker, Vanessa Fuchs, Jens Wendt, Mohsen Ahmadi, Maximilian E. Müller, Riccardo Massei, David Schwartz, Joost Willemse, Bettina Hagen, Thomas Zobel, Susanne Kunis, Peter Zentis, Niraj Kandpal, Tom Boissonnet",https://www.youtube.com/playlist?list=PL2k-L-zWPoR67_02CuEROsYr1nnCNgMcI,"Research Data Management, Include In Dalia",UNKNOWN,"Talk Series RDM4mic Meeting 2025 in Münster, Germany about RDM and the role of NFDI4BIOIMAGE in supporting researchers with tools and services for RDM in bioimaging."
+The Power of Sharing: Open Data in Bio-image Analysis,"Elena Nicolay, Mara Lampert, Frauke Beyer, Ronny Gey, Michaela Unger, Dr. Riccardo Massei",https://www.youtube.com/watch?v=z8MKF4FOjZ4,"Open Data, Fair Principles, Research Data Management, Include In Dalia",UNKNOWN,"The YMIA present a panel discussion on open and FAIR data in the community of bio-image analysis. The event was hosted by Mara Lampert and Elena Nicolay at the UFZ Leipzig on October 24th in 2025. Our panelists were Dr. Frauke Beyer, Ronny Gey, Michaela Unger and Dr. Riccardo Massei (jumped in for Dr. Cornelia Wetzker). Enjoy an interesting conversation of ongoing practices and issues regarding open data in the field of bioimaging."
+DAFT: minimal principles for reproducible research papers,Bruno C. Vellutini,['https://brunovellutini.com/posts/daft-principles/'],"Reproducibility, Fair Principles, Research Data Management, Include In Dalia",CC-BY-SA-4.0,A minimal set of principles for organizing research papers.
+"When To Say ""Good Enough""",Beth Cimini,['https://zenodo.org/records/10498985'],"Bioimage Analysis, Include In Dalia",CC-BY-4.0,"Blog post from the ""Measure Everything... Ask Questions Later"" blog of the Broad Institute Imaging Platform. How do I know when my analysis workflow is doing well enough at finding the objects or measuring the things I care about?"
+The Illustrated Stable Diffusion,Jay Alammar,['https://jalammar.github.io/illustrated-stable-diffusion/'],"Artificial Intelligence, Include In Dalia",CC-BY-NC-SA-4.0,AI image generation is the most recent AI capability blowing people’s minds (mine included). The ability to create striking visuals from text descriptions has a magical quality to it and points clearly to a shift in how humans create art. The release of Stable Diffusion is a clear milestone in this development because it made a high-performance model available to the masses.

_sources/authors/anna_kreshuk.md

@@ -1,4 +1,4 @@
-# Anna kreshuk (6)
+# Anna kreshuk (7)
 ## Developing open-source software for bioimage analysis: opportunities and challenges
 
 Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
@@ -73,6 +73,27 @@ Content type: Slides, Code, Notebook
 [https://github.com/miura/NEUBIAS_AnalystSchool2018](https://github.com/miura/NEUBIAS_AnalystSchool2018)
 
 
+---
+
+## The Crucial Role of BioImage Analysts in Scientific Research and Publication
+
+Beth Cimini, Peter Bankhead, Rocco D'Antuono, Fazeleh Elnaz, Julia Fernandez-Rodriguez, Caterina Fuster-Barceló, Robert Haase, Helena Jambor, Martin L Jones, Florian Jug, Anna Klemm, Anna Kreshuk, Stefania Marcotti, Gabriel G Martins, Sara McArdle, Arrate Muñoz Barrutia, Laura Murphy, Michael Nelson, Simon Nørrelykke, Perrine Paul-Gilloteaux, Thomas Pengo, Joanna Pylvänäinen, Lior Pytowski, Arianna Ravera, Annika Reinke, Yousr Rekik, Caterina Strambio-De-Castillia, Daniel Thédié, Virginie Uhlmann, Oliver Umney, Laura Wiggins, Kevin Eliceiri
+
+Published 2024-06-03
+
+Licensed CC-BY-4.0
+
+
+
+Bioimage analysis (BIA) is a critical discipline in the field of biological research. It overcomes the limitations of subjective analysis in microscopy through the creation of quantitative and reproducible methods. This paper is the result of a recent meeting of bioimage analysts who aimed to summarize the current state of affairs for BIA including categorizing current obstacles and offering possible solutions to them.
+
+Tags: Bioimage Analysis, Include In Dalia
+
+Content type: Publication
+
+[https://zenodo.org/records/11457452](https://zenodo.org/records/11457452)
+
+
 ---
 
 ## The crucial role of bioimage analysts in scientific research and publication

_sources/authors/arina_rybina.md

@@ -43,7 +43,7 @@ European Life Science Research Infrastructures (LS-RIs), one of the five major R
 
 ## Preprint: "Be Sustainable", Recommendations for FAIR Resources in Life Sciences research: EOSC-Life's Lessons
 
-Romain David, Arina Rybina, Jean-Marie Burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Exter Katrina, Sven Fahrener, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjorn Gruning, Kim Tamara Gurwitz, John Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, L. Allyson Lister, Dario Livio Longo, Rebecca Ludwig, Benedicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Mayrhofer Michaela Th., Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S. Richard, Paolo Romano, Antonio Rosato, Alex Sanchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V. Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon
+Romain David, Arina Rybina, jean-marie burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Exter Katrina, Sven Fahrener, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjorn Gruning, Kim Tamara Gurwitz, John Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, L. Allyson Lister, Dario Livio Longo, Rebecca Ludwig, Benedicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Mayrhofer Michaela Th., Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S. Richard, Paolo Romano, Antonio Rosato, Alex Sanchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V. Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon
 
 Published 2023-09-12
 

_sources/authors/beatriz_serrano-solano.md

@@ -225,7 +225,7 @@ European Life Science Research Infrastructures (LS-RIs), one of the five major R
 
 ## Preprint: "Be Sustainable", Recommendations for FAIR Resources in Life Sciences research: EOSC-Life's Lessons
 
-Romain David, Arina Rybina, Jean-Marie Burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Exter Katrina, Sven Fahrener, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjorn Gruning, Kim Tamara Gurwitz, John Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, L. Allyson Lister, Dario Livio Longo, Rebecca Ludwig, Benedicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Mayrhofer Michaela Th., Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S. Richard, Paolo Romano, Antonio Rosato, Alex Sanchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V. Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon
+Romain David, Arina Rybina, jean-marie burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Exter Katrina, Sven Fahrener, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjorn Gruning, Kim Tamara Gurwitz, John Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, L. Allyson Lister, Dario Livio Longo, Rebecca Ludwig, Benedicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Mayrhofer Michaela Th., Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Audrey S. Richard, Paolo Romano, Antonio Rosato, Alex Sanchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Hans V. Westerhoff, Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon
 
 Published 2023-09-12
 

_sources/authors/beth_cimini.md

@@ -0,0 +1,205 @@
+# Beth cimini (10)
+## Bilayers - an easy way to make your favorite deep learning tool more user-friendly
+
+Beth Cimini
+
+Published 2025-01-27
+
+Licensed CC-BY-4.0
+
+
+
+Bilayers as a framework to containerize and describe algorithms/software in deep learning to make it more user-friendly.
+
+Tags: Deep Learning, Include In Dalia
+
+Content type: Slides
+
+[https://zenodo.org/records/14751700](https://zenodo.org/records/14751700)
+
+
+---
+
+## Bioimaging AI Textbook
+
+Rachel Lee, Owen Puls, Wei Ouyang, Beth Cimini
+
+Published 2025-02-20
+
+Licensed BSD-3-CLAUSE
+
+
+
+This is a repository containing a textbook written for BioImaging scientists and other microscopists.
+
+Tags: Bioimage Analysis, Artificial Intelligence, Include In Dalia
+
+Content type: Book, Github Repository
+
+[https://github.com/aicjanelia/BioImagingAI](https://github.com/aicjanelia/BioImagingAI)
+
+
+---
+
+## Creating and troubleshooting microscopy analysis workflows: common challenges and common solutions
+
+Beth Cimini
+
+Published 2024-02-29
+
+Licensed CC-BY-4.0
+
+
+
+As microscopy diversifies and becomes ever-more complex, the problem of quantification of microscopy images has emerged as a major roadblock for many researchers. All researchers must face certainchallenges in turning microscopy images into answers, independent of their scientific question and the images they have generated. Challenges may arise at many stages throughout the analysis process, including handling of the image files, image pre-processing, object finding, or measurement, and statistical analysis. While the exact solution required for each obstacle will be problem-specific, by understanding tools and tradeoffs, optimizing data quality, breaking workflows and data sets into chunks, talking to experts, and thoroughly documenting what has been done, analysts at any experience level can learn to overcome these challenges and create better and easier image analyses.
+
+Tags: Bioimage Analysis, Include In Dalia
+
+Content type: Publication
+
+[https://zenodo.org/records/10734599](https://zenodo.org/records/10734599)
+
+
+---
+
+## Image-based Profiling Handbook
+
+Beth Cimini, Tim Becker, Shantanu Singh, Gregory Way, Hamdah Abbasi, Callum Tromans-Coia
+
+Licensed CC0-1.0
+
+
+
+Tags: Bioimage Analysis, Include In Dalia
+
+Content type: Book
+
+[https://github.com/cytomining/profiling-handbook](https://github.com/cytomining/profiling-handbook)
+
+[https://cytomining.github.io/profiling-handbook/](https://cytomining.github.io/profiling-handbook/)
+
+
+---
+
+## Jupyter Book as a tool for multi-language teaching and training
+
+Beth Cimini
+
+Published 2024-02-13
+
+Licensed CC-BY-4.0
+
+
+
+Can Jupyter Book help make the friendliest possible resource we can think of, in a way that does not get out of date?
+
+Tags: Jupyter Book, Include In Dalia
+
+Content type: Slides
+
+[https://zenodo.org/records/10653464](https://zenodo.org/records/10653464)
+
+
+---
+
+## Microscopy data analysis: machine learning and the BioImage Archive
+
+Andrii Iudin, Anna Foix-Romero, Anna Kreshuk, Awais Athar, Beth Cimini, Dominik Kutra, Estibalis Gomez de Mariscal, Frances Wong, Guillaume Jacquemet, Kedar Narayan, Martin Weigert, Nodar Gogoberidze, Osman Salih, Petr Walczysko, Ryan Conrad, Simone Weyend, Sriram Sundar Somasundharam, Suganya Sivagurunathan, Ugis Sarkans
+
+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: Bioimage Analysis, Python, Artificial Intelligence, Include In Dalia
+
+Content type: Video, Slides
+
+[https://www.ebi.ac.uk/training/materials/microscopy-data-analysis-machine-learning-and-the-bioimage-archive-materials/](https://www.ebi.ac.uk/training/materials/microscopy-data-analysis-machine-learning-and-the-bioimage-archive-materials/)
+
+
+---
+
+## Moving beyond the desktop: Prospects for Practical Bioimage Analysis via the Web
+
+Wei Ouyang, Kevin W Eliceiri, Beth Cimini
+
+Published 2023-06-02
+
+Licensed CC-BY-4.0
+
+
+
+The rapid advancements in biological imaging and the increasing complexity of image data call for a reevaluation of traditional bioimage analysis methods and how these methods are accessed. In our perspective, we argue that transitioning from desktop-based tools to web-based bioimage analysis offers immense opportunities for enhanced accessibility, improved collaboration, and streamlined workflows. We briefly describe the potential advantages, including lower computational requirements and overcoming challenges such as installation issues and limited reproducibility. Additionally, we discuss the current landscape of web-based tools, the challenges in implementation, and the importance of community involvement in driving this transition. By embracing web-based bioimage analysis, we believe the life sciences community can unlock new possibilities for accelerating biological research.
+
+Tags: Bioimage Analysis, Include In Dalia
+
+Content type: Publication
+
+[https://zenodo.org/records/8032892](https://zenodo.org/records/8032892)
+
+
+---
+
+## QI 2024 Analysis Lab Manual
+
+Beth Cimini, Florian Jug, QI 2024
+
+Licensed CC-BY-4.0
+
+
+
+This book contains the quantitative analysis labs for the QI CSHL course, 2024
+
+Tags: Python, Include In Dalia
+
+Content type: Notebook
+
+[https://bethac07.github.io/qi_2024_analysis_lab_manual/intro.html](https://bethac07.github.io/qi_2024_analysis_lab_manual/intro.html)
+
+
+---
+
+## The Crucial Role of BioImage Analysts in Scientific Research and Publication
+
+Beth Cimini, Peter Bankhead, Rocco D'Antuono, Fazeleh Elnaz, Julia Fernandez-Rodriguez, Caterina Fuster-Barceló, Robert Haase, Helena Jambor, Martin L Jones, Florian Jug, Anna Klemm, Anna Kreshuk, Stefania Marcotti, Gabriel G Martins, Sara McArdle, Arrate Muñoz Barrutia, Laura Murphy, Michael Nelson, Simon Nørrelykke, Perrine Paul-Gilloteaux, Thomas Pengo, Joanna Pylvänäinen, Lior Pytowski, Arianna Ravera, Annika Reinke, Yousr Rekik, Caterina Strambio-De-Castillia, Daniel Thédié, Virginie Uhlmann, Oliver Umney, Laura Wiggins, Kevin Eliceiri
+
+Published 2024-06-03
+
+Licensed CC-BY-4.0
+
+
+
+Bioimage analysis (BIA) is a critical discipline in the field of biological research. It overcomes the limitations of subjective analysis in microscopy through the creation of quantitative and reproducible methods. This paper is the result of a recent meeting of bioimage analysts who aimed to summarize the current state of affairs for BIA including categorizing current obstacles and offering possible solutions to them.
+
+Tags: Bioimage Analysis, Include In Dalia
+
+Content type: Publication
+
+[https://zenodo.org/records/11457452](https://zenodo.org/records/11457452)
+
+
+---
+
+## When To Say "Good Enough"
+
+Beth Cimini
+
+Published 2019-10-21
+
+Licensed CC-BY-4.0
+
+
+
+Blog post from the "Measure Everything... Ask Questions Later" blog of the Broad Institute Imaging Platform. How do I know when my analysis workflow is doing well enough at finding the objects or measuring the things I care about?
+
+Tags: Bioimage Analysis, Include In Dalia
+
+Content type: Blog Post
+
+[https://zenodo.org/records/10498985](https://zenodo.org/records/10498985)
+
+
+---
+

_sources/authors/caterina_strambio-de-castillia.md

@@ -1,4 +1,4 @@
-# Caterina strambio-de-castillia (6)
+# Caterina strambio-de-castillia (7)
 ## Community-developed checklists for publishing images and image analyses
 
 Christopher Schmied, Michael S Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T Carvalho, Catalin Chiritescu, Jana Christopher, Beth A Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G Martins, Aastha Mathur, Kota Miura, Paula Montero Llopis, Roland Nitschke, Alison North, Adam C Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T Scott, Arne Seitz, Olaf Selchow, Ved P Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Douglas Taatjes, Christian Tischer, Helena Klara Jambor
@@ -333,6 +333,27 @@ Content type: Publication
 [https://www.nature.com/articles/s41592-021-01290-5](https://www.nature.com/articles/s41592-021-01290-5)
 
 
+---
+
+## The Crucial Role of BioImage Analysts in Scientific Research and Publication
+
+Beth Cimini, Peter Bankhead, Rocco D'Antuono, Fazeleh Elnaz, Julia Fernandez-Rodriguez, Caterina Fuster-Barceló, Robert Haase, Helena Jambor, Martin L Jones, Florian Jug, Anna Klemm, Anna Kreshuk, Stefania Marcotti, Gabriel G Martins, Sara McArdle, Arrate Muñoz Barrutia, Laura Murphy, Michael Nelson, Simon Nørrelykke, Perrine Paul-Gilloteaux, Thomas Pengo, Joanna Pylvänäinen, Lior Pytowski, Arianna Ravera, Annika Reinke, Yousr Rekik, Caterina Strambio-De-Castillia, Daniel Thédié, Virginie Uhlmann, Oliver Umney, Laura Wiggins, Kevin Eliceiri
+
+Published 2024-06-03
+
+Licensed CC-BY-4.0
+
+
+
+Bioimage analysis (BIA) is a critical discipline in the field of biological research. It overcomes the limitations of subjective analysis in microscopy through the creation of quantitative and reproducible methods. This paper is the result of a recent meeting of bioimage analysts who aimed to summarize the current state of affairs for BIA including categorizing current obstacles and offering possible solutions to them.
+
+Tags: Bioimage Analysis, Include In Dalia
+
+Content type: Publication
+
+[https://zenodo.org/records/11457452](https://zenodo.org/records/11457452)
+
+
 ---
 
 ## The crucial role of bioimage analysts in scientific research and publication