Slides (83)#
“ZENODO und Co.” Was bringt und wer braucht ein Repositorium?#
Elfi Hesse, Jan-Christoph Deinert, Christian Löschen
Published 2021-01-25
Licensed CC-BY-4.0
Die Online-Veranstaltung fand am 21.01.2021 im Rahmen der SaxFDM-Veranstaltungsreihe “Digital Kitchen - Küchengespräche mit SaxFDM” statt. SaxFDM-Sprecherin Elfi Hesse (HTW Dresden) erläuterte zunächst Grundsätzliches zum Thema Repositorien. Anschließend teilten Nutzer (Jan Deinert – HZDR) und Anbieter (Christian Löschen – TU Dresden/ZIH) lokaler Repositorien ihre Erfahrungen mit uns.
Tags: Research Data Management
Content type: Slides
A Glimpse of the Open-Source FLIM Analysis Software Tools FLIMfit, FLUTE and napari-flim-phasor-plotter#
Anca Margineanu, Chiara Stringari, Marcelo Zoccoler, Cornelia Wetzker
Licensed CC-BY-4.0
The presentations introduce open-source software to read in, visualize and analyse fluorescence lifetime imaging microscopy (FLIM) raw data developed for life scientists. The slides were presented at German Bioimaging (GerBI) FLIM Workshop held February 26 to 29 2024 at the Biomedical Center of LMU München by Anca Margineanu, Chiara Stringari and Conni Wetzker.
Tags: Bioimage Analysis, Flim
Content type: Slides
AI ML DL in Bioimage Analysis - Webinar#
Yannick KREMPP
Published 2024-11-14
Licensed UNKNOWN
A review of the tools, methods and concepts useful for biologists and life scientists as well as bioimage analysts.
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Video, Slides, Webinar
Adding a Workflow to BIAFLOWS#
Sébastien Tosi, Volker Baecker, Benjamin Pavie
Licensed BSD-2-CLAUSE
Tags: Neubias, Bioimage Analysis
Content type: Slides
Alles meins – oder!? Urheberrechte klären für Forschungsdaten#
Stephan Wünsche
Published 2024-06-04
Licensed CC-BY-4.0
Wem gehören Forschungsdaten? Diese Frage stellt sich bei Daten, an deren Entstehung mehrere Personen beteiligt waren, und besonders bei Textdaten, Bildern und Videos. Hier lernen Sie, für Ihr eigenes Forschungsvorhaben zu erkennen, wessen Urheber- und Leistungsschutzrechte zu berücksichtigen sind. Sie erfahren, wie Sie mit Hilfe von Vereinbarungen frühzeitig Rechtssicherheit herstellen, etwa um Daten weitergeben oder publizieren zu können.
Tags: Research Data Management, Licensing
Content type: Slides
Bio Image Analysis#
Christian Tischer
Licensed UNKNOWN
Content type: Slides
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, Nfdi4Bioimage
Content type: Slides
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: Artificial Intelligence, Python
Content type: Slides
Bio-image Data Science Lectures @ Uni Leipzig / ScaDS.AI#
Robert Haase
Licensed CC-BY-4.0
These are the PPTx training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. The material developed here between April and July 2024.
Tags: Bioimage Analysis, Artificial Intelligence, Python
Content type: Slides
Building a Bioimage Analysis Workflow using Deep Learning#
Estibaliz Gómez-de-Mariscal
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides
CellProfiler Introduction#
Anna Klemm
Licensed UNKNOWN
Tags: Neubias, Cellprofiler, Bioimage Analysis
Content type: Slides
Challenges and opportunities for bio-image analysis core-facilities#
Robert Haase
Licensed CC-BY-4.0
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
Crashkurs Forschungsdatenmanagement#
Barbara Weiner, Stephan Wünsche, Stefan Kühne, Pia Voigt, Sebastian Frericks, Clemens Hoffmann, Romy Elze, Ronny Gey
Published 2020-04-30
Licensed CC-BY-4.0
Diese Präsentation bietet einen Einstieg in alle relevanten Bereiche des Forschungsdatenmanagements an der Universität Leipzig. Behandelt werden Grundlagen des Forschungsdatenmanagements, technische, ethische und rechtliche Aspekte sowie die Archivierung und Publikation von Forschungsdaten. Die Präsentation enthält zahlreiche weiterführende Links (rot) und Literaturhinweise.
Ergänzend hierzu wird eine Präsentation mit Übungsaufgaben angeboten, die helfen soll, das Gelernte zu festigen und in der eigenen Forschungspraxis umzusetzen. Den Aufgaben folgen jeweils eine Antwortfolie sowie deren Auflösung.
Tags: Research Data Management
Content type: Slides
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: Slides
Cultivating Open Training#
Robert Haase
Published 2024-03-14
Licensed CC-BY-4.0
In this SaxFDM Digital Kitchen, I introduced current challenges and potential solutions for openly sharing training materials, softly focusing on bio-image analysis. In this field a lot of training materials circulate in private channels, but openly shared, reusable materials, according to the FAIR-principles, are still rare. Using the CC-BY license and uploading materials to publicly acessible repositories are proposed to fill this gap.
Tags: Open Science, Research Data Management, FAIR-Principles, Bioimage Analysis, Licensing
Content type: Slides
Cultivating Open Training to advance Bio-image Analysis#
Robert Haase
Published 2024-04-25
Licensed CC-BY-4.0
These slides introduce current challenges and potential solutions for openly sharing training materials, focusing on bio-image analysis. In this field a lot of training materials circulate in private channels, but openly shared, reusable materials, according to the FAIR-principles, are still rare. Using the CC-BY license and publicly acessible repositories are proposed to fill this gap.
Tags: Research Data Management, Licensing, FAIR-Principles
Content type: Slides
DL@MBL 2021 Exercises#
Jan Funke, Constantin Pape, Morgan Schwartz, Xiaoyan
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides, Notebook
Data management at France BioImaging#
Published 2023-07-05
Licensed CC-BY-SA-4.0
Tags: Research Data Management, Bioimage Analysis, Open Science
Content type: Slides, Presentation
https://omero-fbi.fr/slides/elmi23_cfd/main.html#/title-slide
Datenmanagement#
Robert Haase
Published 2024-04-14
Licensed CC-BY-4.0
In dieser Data Management Session wird der Lebenszyklus von Daten näher beleuchtet. Wie entstehen Daten, was passiert mit ihnen, wenn sie verarbeitet werden? Wem gehören die Daten und wer ist dafür verantwortlich, sie zu veröffentlichen, zu archivieren und gegebenenfalls wiederzuverwenden? Wir werden einen Datenmanagementplan in Gruppenarbeit entwerfen, ggf. mit Hilfe von ChatGPT.
Tags: Research Data Management
Content type: Slides
Datenmanagement im Fokus: Organisation, Speicherstrategien und Datenschutz#
Pia Voigt, Carolin Hundt
Published 2024-04-19
Licensed CC-BY-4.0
Workshop zum Thema „Datenmanagement im Fokus: Organisation, Speicherstrategien und Datenschutz“ auf der Data Week Leipzig Der Umgang mit Daten ist im Alltag nicht immer leicht: Wie und wo speichert man Daten idealerweise? Welche Strategien helfen, den Überblick zu behalten und wie geht man mit personenbezogenen Daten um? Diese Fragen möchten wir gemeinsam mit Ihnen anhand individueller Datenprobleme besprechen und Ihnen Lösungen aufzeigen, wie Sie ihr Datenmanagement effizient gestalten können.
Tags: Research Data Management
Content type: Slides
Datenmanagementpläne erstellen - Teil 1#
Pia Voigt, Barbara Weiner
Published 2021-03-23
Licensed CC-BY-4.0
Was ist ein Datenmanagementplan? Welche Vorgaben sollte ich beachten? Wie erstelle ich einen solchen für mein Forschungsprojekt und welche nützlichen Tools kann ich hierfür verwenden?
Die Anforderungen der Forschungsförderer zum Datenmanagement steigen stetig. Damit verbunden ist häufig auch das Erstellen eines Datenmanagementplans. Dabei erwarten DFG, BMBF oder die EU jeweils unterschiedliche Angaben zur Erhebung, Speicherung und Veröffentlichung von projektbezogenen Forschungsdaten. Zudem bietet das Erstellen eines Datenmanagementplans viele Vorteile und hilft Ihnen nicht zuletzt, die Anforderungen der guten wissenschaftlichen Praxis strukturiert umzusetzen.
Was im ersten Moment unübersichtlich und überfordernd wirkt, soll in diesem Kurs anhand einer grundlegenden theoretischen Einführung im ersten und praxisorientierter Beispiele im zweiten Teil der Veranstaltung handhabbar gemacht werden. Sie lernen, was hinter den Anforderungen der Forschungsförderer steckt, welche Elemente ein Datenmanagementplan enthalten sollte und wie sie einen solchen mithilfe interaktiver Tools selbst erstellen können.
Tags: Research Data Management
Content type: Slides
Datenmanagementpläne erstellen - Teil 2#
Pia Voigt, Barbara Weiner
Published 2021-03-30
Licensed CC-BY-4.0
Was ist ein Datenmanagementplan? Welche Vorgaben sollte ich beachten? Wie erstelle ich einen solchen für mein Forschungsprojekt und welche nützlichen Tools kann ich hierfür verwenden?
Die Anforderungen der Forschungsförderer zum Datenmanagement steigen stetig. Damit verbunden ist häufig auch das Erstellen eines Datenmanagementplans. Dabei erwarten DFG, BMBF oder die EU jeweils unterschiedliche Angaben zur Erhebung, Speicherung und Veröffentlichung von projektbezogenen Forschungsdaten. Zudem bietet das Erstellen eines Datenmanagementplans viele Vorteile und hilft Ihnen nicht zuletzt, die Anforderungen der guten wissenschaftlichen Praxis strukturiert umzusetzen.
Was im ersten Moment unübersichtlich und überfordernd wirkt, soll in diesem Kurs anhand einer grundlegenden theoretischen Einführung im ersten und praxisorientierter Beispiele im zweiten Teil der Veranstaltung handhabbar gemacht werden. Sie lernen, was hinter den Anforderungen der Forschungsförderer steckt, welche Elemente ein Datenmanagementplan enthalten sollte und wie sie einen solchen mithilfe interaktiver Tools selbst erstellen können.
Version 2 enthält aktuelle Links und weiterführende Hinweise zu einzelnen Aspekten eines Datenmanagementplans.
Version 3 ist die überarbeitete und aktualisierte Version der ersten beiden und enthält u.a. Hinweise zur Lizenzierung und zu Nutzungsrechten an Forschungsdaten.
Tags: Research Data Management
Content type: Slides
Dr Guillaume Jacquemet on studying cancer cell metastasis in the era of deep learning for microscopy#
Guillaume Jacquemet
Published 2024-10-24
Licensed UNKNOWN
Leukocyte extravasation is a critical component of the innate immune response, while circulating tumour cell extravasation is a crucial step in metastasis formation. Despite their importance, these extravasation mechanisms remain incompletely understood. In this talk, Guillaume Jacquemet presents a novel imaging framework that integrates microfluidics with high-speed, label-free imaging to study the arrest of pancreatic cancer cells (PDAC) on human endothelial layers under physiological flow conditions.
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Video, Slides
Einblicke ins Forschungsdatenmanagement - Darf ich das veröffentlichen? Rechtsfragen im Umgang mit Forschungsdaten#
Stephan Wünsche, Pia Voigt
Published 2021-05-11
Licensed CC-BY-4.0
Diese Präsentation wurde im Zuge der digitalen Veranstaltungsreihe “Einblicke ins Forschungsdatenmanagement” erstellt. Diese findet seit dem SS 2020 an der Universität Leipzig für alle Interessierten zu verschiedenen Themen des Forschungsdatenmanagements statt.
Dieser Teil der Reihe dreht sich um Rechtsfragen im Umgang mit Forschungsdaten und deren Bedeutung für die wissenschaftliche Praxis. Sie finden in der vorliegenden Präsentation einen Überblick über relevante Rechtsbereiche sowie Erläuterungen zum Datenschutz, Urheberrecht und den Grundsätzen der guten wissenschaftlichen Praxis mit Fokus auf deren Bedeutung im Forschungsdatenmanagement.
Tags: Research Data Management, Data Protection
Content type: Slides
Euro-BioImaging’s Guide to FAIR BioImage Data - Practical Tasks#
Isabel Kemmer, Euro-BioImaging ERIC
Published 2024-06-04
Licensed CC-BY-4.0
Hands-on exercises on FAIR Bioimage Data from the interactive online workshop “Euro-BioImaging’s Guide to FAIR BioImage Data 2024” (https://www.eurobioimaging.eu/news/a-guide-to-fair-bioimage-data-2024/). Types of tasks included: FAIR characteristics of a real world dataset Data Management Plan (DMP) Journal Policies on FAIR data sharing Ontology search Metadata according to REMBI scheme (Image from: Sarkans, U., Chiu, W., Collinson, L. et al. REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology. Nat Methods 18, 1418–1422 (2021). https://doi.org/10.1038/s41592-021-01166-8) Matching datasets to bioimage repositories Browsing bioimage repositories
Tags: Bioimage Analysis, FAIR-Principles, Research Data Management
Content type: Slides, Tutorial
FAIRy deep-learning for bioImage analysis#
Estibaliz Gómez de Mariscal
Licensed CC-BY-4.0
Introduction to FAIR deep learning. Furthermore, tools to deploy trained DL models (deepImageJ), easily train and evaluate them (ZeroCostDL4Mic and DeepBacs) ensure reproducibility (DL4MicEverywhere), and share this technology in an open-source and reproducible manner (BioImage Model Zoo) are introduced.
Tags: Artificial Intelligence, FAIR-Principles, Bioimage Analysis
Content type: Slides
Galaxy Training Material#
Licensed MIT
Content type: Slides, Tutorial
Generative artificial intelligence for bio-image analysis#
Robert Haase
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis, Artificial Intelligence
Content type: Slides
Hackaton Results - Conversion of KNIME image analysis workflows to Galaxy#
Riccardo Massei
Licensed CC-BY-4.0
Results of the project ‘Conversion of KNIME image analysis workflows to Galaxy’ during the Hackathon ‘Image Analysis in Galaxy’ (Freiburg 26 Feb - 01 Mar 2024)
Tags: Research Data Management
Content type: Slides
Hitchhiking through a diverse Bio-image Analysis Software Universe#
Robert Haase
Published 2022-07-22
Licensed CC-BY-4.0
Overview about decision making and how to influence decisions in the bio-image analysis software context.
Tags: Bioimage Analysis
Content type: Slides, Presentation
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: Slides, 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: Slides
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: Slides
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: Slides, Code
ImageJ2 API-beating#
Robert Haase
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slides
Intro napari slides#
Peter Sobolewski
Licensed MIT
Introduction to napari workshop run at JAX (Spring 2024).
Tags: Napari
Content type: Slides
https://thejacksonlaboratory.github.io/intro-napari-slides/#/section
Introduction to ImageJ macro programming, Scientific Computing Facility, MPI CBG Dresden#
Robert Haase, Benoit Lombardot
Licensed UNKNOWN
Tags: Imagej, Bioimage Analysis
Content type: Slides
Introduction to Research Data Management and Open Research#
Shanmugasundaram
Published 2024-05-17
Licensed CC-BY-4.0
Introduction to RDM primarily for researchers. Can be seen as primer to all other materials in this catalogue.
Tags: Research Data Management, Open Science
Content type: Slides
Jupyter for interactive cloud computing#
Guillaume Witz
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slides
Kollaboratives Arbeiten und Versionskontrolle mit Git#
Robert Haase
Published 2024-04-15
Licensed CC-BY-4.0
Gemeinsames Arbeiten im Internet stellt uns vor neue Herausforderungen: Wer hat eine Datei wann hochgeladen? Wer hat zum Inhalt beigetragen? Wie kann man Inhalte zusammenfuehren, wenn mehrere Mitarbeiter gleichzeitig Aenderungen gemacht haben? Das Versionskontrollwerkzeug git stellt eine umfassende Loesung fuer solche Fragen bereit. Die Onlineplatform github.com stellt nicht nur Softwareentwicklern weltweit eine git-getriebene Platform zur Verfuegung und erlaubt ihnen effektiv zusammen zu arbeiten. In diesem Workshop lernen wir:
Infuerung in FAIR-Prinzipien im Softwarecontext Arbeiten mit git: Pull-requests Aufloesen von Merge-Konflikten Automatisiertes Archivieren von Inhalten nach Zenodo.org Eigene Webseiten auf github.io publizieren
Tags: Research Data Management, FAIR-Principles, Git, Zenodo
Content type: Slides
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: Slides
https://git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis
Lecture-materials of the DeepLife course#
Carl Herrmann, annavonbachmann, David Hoksza, Martin Schätz, Dario Malchiodi, jnguyenvan, Britta Velten, Elodie Laine, JanaBraunger, barwil
Published 2023-12-06
Licensed UNKNOWN
Tags: Bioinformatics
Content type: Github Repository, Slides, Notebook
Machine Learning - Deep Learning. Applications to Bioimage Analysis#
Estibaliz Gómez-de-Mariscal
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides
Machine and Deep Learning on the cloud: Segmentation#
Ignacio Arganda-Carreras
Licensed UNKNOWN
Tags: Neubias, Artificial Intelligence, Bioimage Analysis
Content type: Slides
Methods in bioimage analysis#
Christian Tischer
Licensed CC-BY-4.0
Tags: Bioimage Analysis
Content type: Online Tutorial, Video, Slides
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
MicroSam-Talks#
Constantin Pape
Published 2024-05-23
Licensed CC-BY-4.0
Talks about Segment Anything for Microscopy: computational-cell-analytics/micro-sam. Currently contains slides for two talks:
Overview of Segment Anythign for Microscopy given at the SWISSBIAS online meeting in April 2024 Talk about vision foundation models and Segment Anything for Microscopy given at Human Technopole as part of the EMBO Deep Learning Course in May 2024
Tags: Bioimage Analysis, Artificial Intelligence
Content type: Slides
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
Content type: Video, Slides
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: Slides
https://git.mpi-cbg.de/rhaase/lecture_multiview_registration
Multiplexed tissue imaging - tools and approaches#
Agustín Andrés Corbat, OmFrederic, Jonas Windhager, Kristína Lidayová
Licensed CC-BY-4.0
Material for the I2K 2024 “Multiplexed tissue imaging - tools and approaches” workshop
Tags: Bioimage Analysis
Content type: Github Repository, Slides, Workshop
BIIFSweden/I2K2024-MTIWorkshop
https://docs.google.com/presentation/d/1R9-4lXAmTYuyFZpTMDR85SjnLsPZhVZ8/edit#slide=id.p1
My Journey Through Bioimage Analysis Teaching Methods From Classroom to Cloud#
Elnaz Fazeli
Published 2024-02-19
Licensed CC-BY-4.0
In these slides I introducemy journey through teaching bioimage analysis courses in different formats, from in person courses to online material. I have an overview of different training formats and comparing these for different audiences.
Tags: Teaching
Content type: Slides
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: Slides, 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: Slides, 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: Slides, 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: Slides, Code, Notebook
NFDI4BIOIMAGE#
Carsten Fortmann-Grote
Licensed CC-BY-4.0
Presentation was given at the 2nd MPG-NFDI Workshop on April 18th about e NFDI4BIOIMAGE Consortium, FAIRification of Image (meta)data, Zarr, RFC, Training (TA5), contributing.
Tags: Research Data Management, Bioimage Analysis, FAIR-Principles, Zarr, Nfdi4Bioimage
Content type: Slides
NFDI4BIOIMAGE - An Initiative for a National Research Data Infrastructure for Microscopy Data#
Christian Schmidt, Elisa Ferrando-May
Published 2021-04-29
Licensed CCY-BY-SA-4.0
Align existing and establish novel services & solutions for data management tasks throughout the bioimage data lifecycle.
Tags: Nfdi4Bioimage, Research Data Management
Content type: Conference Abstract, Slides
NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and BioImage Analysis - Online Kick-Off 2023#
Stefanie Weidtkamp-Peters
Licensed CC-BY-4.0
NFDI4BIOIMAGE core mission, bioimage data challenge, task areas, FAIR bioimage workflows.
Tags: Research Data Management, FAIR-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and BioImage Analysis [conference talk: The Pelagic Imaging Consortium meets Helmholtz Imaging, 5.10.2023, Hamburg]#
Riccardo Massei
Licensed CC-BY-4.0
NFDI4BIOIMAGE is a consortium within the framework of the National Research Data Infrastructure (NFDI) in Germany. In this talk, the consortium and the contribution to the work programme by the Helmholtz Centre for Environmental Research (UFZ) in Leipzig are outlined.
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
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: Slides, 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: Slides
Object Tracking and Track Analysis using TrackMate and CellTracksColab#
Joanna Pylvänäinen
Published None
Licensed GPL-3.0
I2K 2024 workshop materials for “Object Tracking and Track Analysis using TrackMate and CellTracksColab”
Tags: Bioimage Analysis
Content type: Github Repository, Tutorial, Workshop, Slides
Open Science, Sharing & Licensing#
Robert Haase
Published 2024-04-18
Licensed CC-BY-4.0
Wir tauchen ein in die Welt der Open Science und definieren Begriffe wie Open Source, Open Access und die FAIR-Prinzipien (Findable, Accessible, Interoperable and Reuasable). Wir diskutieren, wie diese Methoden der [wissenschaftlichen] Kommunikation und des Datenmanagements die Welt verändern und wie wir sie praktisch in unsere Arbeit integrieren können. Dabei spielen Aspekte wie Copyright und Lizenzierung eine wichtige Rolle.
Tags: Research Data Management, Open Access, FAIR-Principles, Licensing
Content type: Slides
Parallelization and heterogeneous computing: from pure CPU to GPU-accelerated image processing#
Robert Haase
Licensed CC-BY-4.0
Content type: Slides
Promoting Reproducibility in Biomedical Research through Image Analysis#
David Barry
Published 2025-01-29
Licensed CC-BY-4.0 INTERNATIONAL
Slides presented at Empowering Healthcare with Automated Analysis at London Metropolitan University.
Tags: Reproducibility, Image Analysis
Content type: Slides
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: Slides
RDF as a bridge to domain-platforms like OMERO, or There and back again.#
Josh Moore, Andra Waagmeester, Kristina Hettne, Katherine Wolstencroft, Susanne Kunis
Licensed CC-BY-4.0
In 2005, the first version of OMERO stored RDF natively. However, just a year after the 1.0 release of RDF, performance considerations led to the development of a more traditional SQL approach for OMERO. A binary protocol makes it possible to query and retrieve metadata but the resulting information cannot immediately be combined with other sources. This is the adventure of rediscovering the benefit of RDF triples as a – if not the – common exchange mechanism.
Tags: Research Data Management, FAIR-Principles, Bioimage Analysis
Content type: Slides
Research Data Management Seminar - Slides#
Stefano Della Chiesa
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: Slides
So geschlossen wie nötig, so offen wie möglich - Datenschutz beim Umgang mit Forschungsdaten#
Pia Voigt
Published 2024-05-30
Licensed CC-BY-4.0
Der Umgang mit personenbezogenen Daten stellt Forschende oft vor rechtliche Herausforderungen: Unter welchen Bedingungen dürfen personenbezogene Daten verarbeitet werden? Welche Voraussetzungen müssen erfüllt sein und welche Strategien können angewendet werden, um Daten sicher speichern, verarbeiten, teilen und aufbewahren zu können? Mit Hilfe dieses Foliensatzes erhalten Sie Einblicke in datenschutzrechtliche Aspekte beim Umgang mit Ihren Forschungsdaten.
Tags: Research Data Management, Data Protection, FAIR-Principles
Content type: Slides
Sustainable Data Stewardship#
Stefano Della Chiesa
Published 2024-03-25
Licensed CC-BY-4.0
These slides were presented at the 2. SaxFDM-Beratungsstammtisch and delve into the strategic integration of Research Data Management (RDM) within research organizations. The Leibniz IOER presented an insightful overview of RDM activities and approaches, emphasizing the criticality of embedding RDM strategically within research institutions. The presentation showcases some best practices in RDM implementation through practical examples, offering valuable insights for optimizing data stewardship processes.
Tags: Research Data Management, Data Stewardship
Content type: Slides
Thinking data management on different scales#
Susanne Kunis
Licensed CC-BY-4.0
Presentation given at PoL BioImage Analysis Symposium Dresden 2023
Tags: Research Data Management, Nfdi4Bioimage
Content type: Slides
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: Slides
Welcome to BioImage Town#
Josh Moore
Licensed CC-BY-4.0
Welcome at NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, October 16, 2023
Tags: OMERO, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
What is Bioimage Analysis? An Introduction#
Kota Miura
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slides
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: Slides
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: Slides
YMIA - Python-Based Event Series Training Material#
Riccardo Massei, Robert Haase, ENicolay
Published None
Licensed MIT
This repository offer access to teaching material and useful resources for the YMIA - Python-Based Event Series.
Tags: Python, Artifical Intelligence, Bioimage Analysis
Content type: Github Repository, Slides
ZIDAS 2020 Introduction to Deep Learning#
Estibaliz Gómez-de-Mariscal
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides
[N4BI AHM] Welcome to BioImage Town#
Josh Moore
Published 2023-10-16
Licensed CC-BY-4.0
Keynote at the NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, October 16, 2023.
Tags: Research Data Management
Content type: Slides
[Short Talk] NFDI4BIOIMAGE - A consortium in the National Research Data Infrastructure#
Christian Schmidt
Licensed CC-BY-4.0
Short Talk about the NFDI4BIOIMAGE consortium presented at the RDM in (Bio-)Medicine Information Event on April 10th, 2024, organized C³RDM & ZB MED.
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
ilastik: interactive machine learning for (bio)image analysis#
Anna Kreshuk, Dominik Kutra
Licensed CC-BY-4.0
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slides
rse-skills-workshop#
Jack Atkinson
Published 2023-12-22T17:39:48+00:00
Licensed GPL-3.0
Teaching materials for improving research software writing abilities.
Tags: Research Software Engineering
Content type: Github Repository, Slides
jatkinson1000/rse-skills-workshop