Slide (39)#
Adding a Workflow to BIAFLOWS#
[‘Sébastien Tosi’, ‘Volker Baecker’, ‘Benjamin Pavie’]
Licensed BSD-2-CLAUSE
Tags: Neubias, Bioimage Analysis
Content type: Slide
Bio Image Analysis#
[‘Christian Tischer’]
Licensed UNKNOWN
Tags: Bioimage Analysis
Content type: Slide
Bio-Image Data Strudel for Workshop on Research Data Management in TU Dresden Core Facilities#
[‘Cornelia Wetzker’]
Published 2023-11-08
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
Content type: Slide
Bio-image Analysis with the Help of Large Language Models#
[‘Robert Haase’]
Published 2024-03-13
Licensed CC-BY-4.0
Large Language Models (LLMs) change the way how we use computers. This also has impact on the bio-image analysis community. We can generate code that analyzes biomedical image data if we ask the right prompts. This talk outlines introduces basic principles, explains prompt engineering and how to apply it to bio-image analysis. We also compare how different LLM vendors perform on code generation tasks and which challenges are ahead for the bio-image analysis community.
Tags: Large Language Models, Python
Content type: Slide
Building a Bioimage Analysis Workflow using Deep Learning#
[‘Estibaliz Gómez-de-Mariscal']
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
CellProfiler Introduction#
[‘Anna Klemm’]
Licensed UNKNOWN
Tags: Neubias, Cellprofiler, Bioimage Analysis
Content type: Slide
Challenges and opportunities for bio-image analysis core-facilities#
[‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Research Data Management, Bio-Image Analysis, Nfdi4Bioimage
Content type: Slide
Creating open computational curricula#
[‘Kari Jordan’, ‘Zhian Kamvar’, ‘Toby Hodges’]
Published 2020-12-11
Licensed CC-BY-4.0
In this interactive session, Carpentries team members will guide attendees through three stages of the backward design process to create a lesson development plan for the open source tool of their choosing. Attendees will leave having identified what practical skills they aim to teach (learning objectives), an approach for designing challenge questions (formative assessment), and mechanisms to give and receive feedback.
Content type: Slide
DL@MBL 2021 Exercises#
[‘Jan Funke’, ‘Constantin Pape’, ‘Morgan Schwartz’, ‘Xiaoyan’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide, Notebook
Generative artificial intelligence for bio-image analysis#
[‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis, Artificial Intelligence
Content type: Slide
I3D:bio’s OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training#
[‘Christian Schmidt’, ‘Michele Bortolomeazzi’, ‘Tom Boissonnet’, ‘Carsten Fortmann-Grote’, ‘Julia Dohle’, ‘Peter Zentis’, ‘Niraj Kandpal’, ‘Susanne Kunis’, ‘Thomas Zobel’, ‘Stefanie Weidtkamp-Peters’, ‘Elisa Ferrando-May’]
Published 2023-11-13
Licensed CC-BY-4.0
The open-source software OME Remote Objects (OMERO) is a data management software that allows storing, organizing, and annotating bioimaging/microscopy data. OMERO has become one of the best-known systems for bioimage data management in the bioimaging community. The Information Infrastructure for BioImage Data (I3D:bio) project facilitates the uptake of OMERO into research data management (RDM) practices at universities and research institutions in Germany. Since the adoption of OMERO into researchers’ daily routines requires intensive training, a broad portfolio of training resources for OMERO is an asset. On top of using the OMERO guides curated by the Open Microscopy Environment Consortium (OME) team, imaging core facility staff at institutions where OMERO is used often prepare additional material tailored to be applicable for their own OMERO instances. Based on experience gathered in the Research Data Management for Microscopy group (RDM4mic) in Germany, and in the use cases in the I3D:bio project, we created a set of reusable, adjustable, openly available slide decks to serve as the basis for tailored training lectures, video tutorials, and self-guided instruction manuals directed at beginners in using OMERO. The material is published as an open educational resource complementing the existing resources for OMERO contributed by the community.
Tags: Omero, Research Data Management, Nfdi4Bioimage, I3Dbio
Content type: Slide, Video
https://zenodo.org/records/8323588
https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU
Image Data Services at Euro-BioImaging: Community efforts towards FAIR Image Data and Analysis Services#
[‘Aastha Mathur’]
Licensed UNKNOWN
Content type: Slide
https://docs.google.com/presentation/d/1henPIDTpHT3bc1Y26AltItAHJ2C5xCOl/edit#slide=id.p1
Image analysis in Galaxy#
[‘Beatriz Serrano-Solano’, ‘Björn Grüning’]
Licensed UNKNOWN
Tags: Bioimage Analysis
Content type: Slide
https://docs.google.com/presentation/d/1WG_4307XmKsGfWT3taxMvX2rZiG1k0SM1E7SAENJQkI/edit#slide=id.p
ImageJ Macro Introduction#
[‘Anna Klemm’]
Licensed UNKNOWN
Tags: Neubias, Imagej Macro, Bioimage Analysis
Content type: Slide, Code
ImageJ2 API-beating#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
Introduction to ImageJ macro programming, Scientific Computing Facility, MPI CBG Dresden#
[‘Robert Haase’, ‘Benoit Lombardot’]
Licensed UNKNOWN
Tags: Imagej, Bioimage Analysis
Content type: Slide
Jupyter for interactive cloud computing#
[‘Guillaume Witz’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide
Lecture Applied Bioimage Analysis 2020#
[‘Robert Haase’]
Slides, scripts, data and other exercise materials of the BioImage Analysis lecture at CMCB TU Dresden 2020
Tags: Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis
Machine Learning - Deep Learning. Applications to Bioimage Analysis#
[‘Estibaliz Gómez-de-Mariscal’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
Machine and Deep Learning on the cloud: Segmentation#
[‘Ignacio Arganda-Carreras’]
Licensed UNKNOWN
Tags: Neubias, Artificial Intelligence, Bioimage Analysis
Content type: Slide
Methods in bioimage analysis#
[‘Christian Tischer’]
Licensed CC-BY-4.0
Tags: Bioimage Analysis
Content type: Online Tutorial, Video, Slide
https://www.ebi.ac.uk/training/events/methods-bioimage-analysis/
https://doi.org/10.6019/TOL.BioImageAnalysis22-w.2022.00001.1
https://drive.google.com/file/d/1MhuqfKhZcYu3bchWMqogIybKjamU5Msg/view
Multi-view fusion#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Lecture slides of a session on Multiview Fusion in Fiji
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_multiview_registration
NEUBIAS Analyst School 2018#
[‘Assaf Zaritsky’, ‘Csaba Molnar’, ‘Vasja Urbancic’, ‘Richard Butler’, ‘Anna Kreshuk’, ‘Vannary Meas-Yedid’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide, Code, Notebook
NEUBIAS Bioimage Analyst Course 2017#
[‘Curtis Rueden’, ‘Florian Levet’, ‘J.B. Sibarta’, ‘Alexandre Dafour’, ‘Daniel Sage’, ‘Sebastien Tosi’, ‘Michal Kozubek’, ‘Jean-Yves Tinevez’, ‘Kota Miura’, ‘et al.’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide, Tutorial
NEUBIAS Bioimage Analyst School 2019#
[‘Kota Miura’, ‘Chong Zhang’, ‘Jean-Yves Tinevez’, ‘Robert Haase’, ‘Julius Hossein’, ‘Pejamn Rasti’, ‘David Rousseau’, ‘Ignacio Arganda-Carreras’, ‘Siân Culley’, ‘et al.’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide, Code, Notebook
NEUBIAS Bioimage Analyst School 2020#
[‘Marion Louveaux’, ‘Stéphane Verger’, ‘Arianne Bercowsky Rama’, ‘Ignacio Arganda-Carreras’, ‘Estibaliz Gómez-de-Mariscal’, ‘Kota Miura’, ‘et al.’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide, Code, Notebook
Neubias Academy 2020: Introduction to Nuclei Segmentation with StarDist#
[‘Martin Weigert’, ‘Olivier Burri’, ‘Siân Culley’, ‘Uwe Schmidt’]
Licensed UNKNOWN
Tags: Python, Neubias, Artificial Intelligence, Bioimage Analysis
Content type: Slide, Notebook
Nextflow: Scalable and reproducible scientific workflows#
[‘Floden Evan’, ‘Di Tommaso Paolo’]
Published 2020-12-17
Licensed CC-BY-4.0
Nextflow is an open-source workflow management system that prioritizes portability and reproducibility. It enables users to develop and seamlessly scale genomics workflows locally, on HPC clusters, or in major cloud providers’ infrastructures. Developed since 2014 and backed by a fast-growing community, the Nextflow ecosystem is made up of users and developers across academia, government and industry. It counts over 1M downloads and over 10K users worldwide.
Tags: Workflow Engine
Content type: Slide
Parallelization and heterogeneous computing: from pure CPU to GPU-accelerated image processing#
[‘Robert Haase’]
Licensed CC-BY-4.0
Content type: Slide
QuPath: Open source software for analysing (awkward) images#
[‘Peter Bankhead’]
Published 2020-12-16
Licensed CC-BY-4.0
Slides from the CZI/EOSS online meeting in December 2020.
Tags: Bioimage Analysis
Content type: Slide
Research Data Management Seminar - Slides#
[‘Della Chiesa’, ‘Stefano’]
Published 2022-05-18
Licensed CC-BY-4.0
This Research Data Management (RDM) Slides introduce to the multidisciplinary knowledge and competencies required to address policy compliance and research data management best practices throughout a project lifecycle, and beyond it.
Module 1 - Introduces the RDM giving its context in the Research Data Governance
Module 2 - Illustrates the most important RDM policies and principles
Module 3 - Provides the most relevant RDM knowledge bricks
Module 4 - Discuss the Data Management Plans (DMPs), examples, templates and guidance
Tags: Research Data Management
Content type: Slide
Thinking data management on different scales#
[‘Susanne Kunis’]
Published 2023-08-31
Licensed CC-BY-4.0
Presentation given at PoL BioImage Analysis Symposium Dresden 2023
Tags: Research Data Management, Nfdi4Bioimage
Content type: Slide
Tracking Theory, TrackMate, and Mastodon#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Lecture slides of a session on Cell Tracking in Fiji
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
What is Bioimage Analysis? An Introduction#
[‘Kota Miura’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide
https://www.dropbox.com/s/5abw3cvxrhpobg4/20220923_DefragmentationTS.pdf?dl=0
Working with objects in 2D and 3D#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d
Working with pixels#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
ZIDAS 2020 Introduction to Deep Learning#
[‘Estibaliz Gómez-de-Mariscal’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
ilastik: interactive machine learning for (bio)image analysis#
[‘Anna Kreshuk’, ‘Dominik Kutra’]
Licensed CC-BY-4.0
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
https://zenodo.org/doi/10.5281/zenodo.4330625