Recently added (10)#
Bio-image Data Science Lectures 2025 @ Uni Leipzig / ScaDS.AI#
Robert Haase
Published 2025-07-10
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 will develop here and in the corresponding github repository between April and July 2025.
BioImage Analysis and Superresolution Microscopy Workshop 2023 (at Dartmouth College)#
Zuzana Burdíková, Zdeněk Švindrych, Martin Schätz, Jakub Soukup, Pat Robison
Published 2023-06-07
Licensed CC-BY-4.0
The full program is available in the repository (Schedule DMW 2023.rtf) with most of the presentations and all exercises. All exercise files are in ZIP files Data.zip and ThunderSTORM sample data 2023.zip.
Date: June 6-7, 2023 Time: 9am - 5pm Location: Dartmouth College, 74 College St, Hanover, Kellogg 200 Sponsor: bioMT (Lunch and coffee breaks)
Summary: The BioImage Analysis and Superresolution Microscopy Workshop 2023 took place at Dartmouth College, offering participants a comprehensive learning experience in the field of bioimage analysis and superresolution microscopy. Over the course of two days, researchers, scientists, and students immersed themselves in cutting-edge microscopy techniques and expanded their knowledge and practical skills.
Day 1 (Tue, June 6): The workshop began with Zdenek Svindrych providing an overview of microscopy principles, methods, and theoretical foundations. Participants gained insights into image formation in fluorescence microscopes, resolution, and noise. This was followed by an introduction to superresolution microscopy techniques, including Single-Molecule localization Microscopy (STORM, PALM, DNA-PAINT) and Structured Illumination Microscopy (SIM, ISM, Airyscan, SoRa). Zuzana Burdikova then guided attendees through the theoretical aspects of bioimage processing in Fiji, covering image formats, multi-dimensional image analysis, data visualization, and quantitative analysis. Practical sessions allowed participants to apply their knowledge, exploring two-channel colocalization, image filtering, and quantitative measurements in Fiji.
Day 2 (Wed, June 7): The second day commenced with a remote presentation by SVI.nl, introducing participants to the Huygens deconvolution software used in widefield, confocal, and superresolution microscopy. Zdenek Svindrych demonstrated the practical applications of ThunderSTORM, an ImageJ plug-in for single molecule localization microscopy (SMLM) data analysis and superresolution imaging. The session included an overview of the ThunderSTORM workflow, covering localization, filtering, rendering, and 3D STORM using the astigmatism method. Jakub Soukup explored advanced noise reduction algorithms such as Noise2Void and StarDist. Martin Schätz discussed data management strategies.
In the afternoon, participants engaged in practical sessions. Martin Schätz presented Ilastik, a versatile software for image classification and segmentation. Pat Robison delivered a scientific lecture on the role of detyrosinated microtubules in contracting cardiomyocytes. Zdenek Svindrych, along with other experts, led a hands-on session on customizing Fiji using the ImageJ Macro language. The day concluded with a practical session on the interactive design of GPU-accelerated image data flow graphs in Fiji, guided by Martin Schätz and the workshop team.
DNG in BioFormat opens in wrong resolution#
Michael
Published 2025-07-15
Licensed CC-BY-4.0
FAQ Künstliche Intelligenz und gute wissenschaftliche Praxis#
Katrin Frisch
Published 2024-11-06
Licensed CC-BY-4.0
Diese FAQ versammeln Fragen, die uns häufig im Zusammenhang mit künstlicher Intelligenz (KI) und guter wissenschaftlicher Praxis (GWP) erreichen. Die Antworten sollen bei der Orientierung in einem schnelllebigen Thema helfen, ohne dabei präskriptiv zu sein. Sie stellen keine offizielle Positionierung des Ombudsman für die Wissenschaft (OfdW) dar, sondern beschreiben den Status Quo und ordnen bereits bestehende Empfehlungen aus Sicht der GWP ein, identifizieren Lücken und verweisen auf weiterführende Literatur. Diese FAQ-Sammlung richtet sich primär an Forschende. Für die Nutzung von KI in der Lehre und in studentischen (Qualifikations-)Arbeiten sind i.d.R. universitäre KI-Richtlinien, angepasste Prüfungsordnungen und Selbstständigkeitserklärungen sowie Entscheidungen individueller Lehrpersonen maßgeblich. Daher werden eventuelle Besonderheiten von KI in der Lehre und in Prüfungsangelegenheiten in diesen FAQ nicht besprochen.
Internal ALM BioImage Analysis workshop 2023#
Martin Schätz, Maria Azevedo, Paula Sampaio
Published 2023-11-03
Licensed CC-BY-4.0
Internal ALM BioImage Analysis Workshop 2023OverviewThe Internal ALM BioImage Analysis Workshop 2023, organized by the Advanced Light Microscopy i3S scientific platform, was a comprehensive 2.5-day internal workshop dedicated to open-source BioImage Analysis. The event combined informative presentations with hands-on sessions, utilizing the EMBL Bioimage Analysis Desktop (BAND) Platform. The used sources for datasets and presentations are in Notes.Workshop ProgramDay 1: Foundations of BioImage AnalysisIntroduction to Research Data Management [00i3S_Data_Management_2023_MP_Slido]: An exploration of data management, naming conventions, and ethical considerations in BioImage Analysis and image manipulation. Referencing content from the NEUBIASAcademy@Home Webinar: “In Defense of Image Data & Analysis Integrity.”Interactive Image Data Flow Graphs with CLIJ2 in FIJI [01i3S_Interactive Image Data Flow Graphs]: A hands-on session introducing CLIJ2 in FIJI, with a focus on practical applications. Relevant datasets were explored during the presentation, and are described in notes.Day 2: Advanced Techniques in BioImage AnalysisNoise2Void Denoising with CSBdeep in FIJI [02i3S_IMCF_noise2void_EN] : Exploring the Noise2Void denoising approach using the CSBdeep FIJI plugin, with hands-on examples using data from the juglab/n2v GitHub repository.StarDist for Fluorescence Nuclei Segmentation [03i3S_schatzm_stardist_21] : An introduction to StarDist through the FIJI StarDist plugin, with hands-on experience using the BBBC004 dataset.Introduction to Napari 2023 [04i3S_Introduction to Napari 2023] : A hands-on session introducing Napari and its connection with CLIJ2. The datasets used were detailed in the presentation.Ilastik Pixel Classification and BioImage Model Zoo [05i3S_schatzm_Ilastik_woHandOn_PixObj_2023]: Hands-on exploration of Ilastik with a focus on pixel and object classification. Neural networks from the BioImage Model Zoo were also introduced.BioImage Model Zoo Possibilities [06i3S_BioImageModelZoo-Kreshuk]: An overview of the concept of BioImage Model Zoo and its potential applications.DeepImageJ Plugin with Hands-on on Stardist and Unet NNs [07i3S_deepImageJ-Gomez_de_Mariscal]: Introduction to the deepImageJ plugin, capable of utilizing models from the BioImage Model Zoo. The hands-on session focused on Stardist and Unet Neural Networks.Day 3: Practical Applications and Advanced TrainingHands-on with Ilastik Neural Networks: Utilizing BioImage Model Zoos, participants engaged in hands-on exercises using the Ilastik Multicut method from the AdvanceImageAnalysisEMBO2023 GitHub repository.Hands-on with Cellpose 2.0: Practical sessions included applying pre-trained models with the Simple Visual Cellpose Cheat Sheet. Participants also had the opportunity to train new models using original Cellpose datasets and larger data from BBBC019 and BBBC003 datasets. This workshop would not be possible without the previous excellent work of many people involved in the Network of European BioImage Analysts - NEUBIAS and without my attendance at the EMBO Practical Course Advanced methods in bioimage analysis .
Masterclasses from the Euro-Bioimaging EVOLVE Mentoring programme 2025#
Euro-BioImaging ERIC
Published 2025-06-26
Licensed CC-BY-4.0
EVOLVE Mentoring Masterclasses Description:This series captures the class guides of the 2025 masterclasses from Euro‑BioImaging’s EVOLVE Mentoring Program. Included Masterclasses:
Peter O’Toole – “Entrepreneurship & Leadership in Imaging Core Facilities” Peter O’Toole, President of the Royal Microscopical Society and Director of the Bioscience Technology Facility (University of York), kicks off the series with a deep dive into entrepreneurial leadership. He highlights how to balance science, business, and technology, emphasizing stakeholder engagement, staff investment, cross-training, and using social media to boost visibility and unlock funding. Ilaria Testa – “Interdisciplinary Science, SMART Microscopy & Team Building” Professor Ilaria Testa (SciLifeLab & KTH) reflects on her transition from physics to super-resolution microscopy and team leadership. Her session underscores the power of crossing disciplinary boundaries, mentorship, and innovation in live-cell imaging . Daphna Link‑Sourani – “Leadership, Facility Management & Work‑Life Balance” Dr. Daphna Link‑Sourani (Technion Human MRI Research Center) challenges hierarchical notions of leadership, advocating instead for integrity, empathy, and strategic vision. She draws on her experience establishing an MRI facility to discuss crisis management, user engagement, and balancing career demands. Muriel Mari – “Women in Science: Normalizing, Supporting & Leading” Dr. Muriel Mari (Aarhus University) leads a powerful reflection on gender equity in science. Her masterclass goes beyond barriers—focusing on cultural shifts, inclusive leadership, and redefining success. She encourages institutions and individuals alike to move from tokenism to transformative support, and to recognize the diverse paths women take in STEM. Sylvia E. Le Dévédec – “Image Data Management & FAIR Core Facilities” Dr. Sylvia Le Dévédec (Leiden University) discusses how to integrate FAIR data principles in imaging core facilities. Drawing on her experience with high-content imaging and Open Science advocacy, she outlines actionable steps toward sustainable, reusable, and accessible data workflows.
Why Archive These Sessions?These masterclasses offer invaluable insights for core facility managers, imaging scientists, and team leaders in life sciences. They blend hands-on leadership strategies, technical facility growth advice, and real-world experience—making them essential viewing for professionals and institutions aiming to build sustainable, people-centred imaging infrastructures.
Open source AI Tools for bioimage analysis workshop (2024) @ICOB, Academia Sinica, Taiwan#
Wei-Chen Chu
Published 2024-08-09
Licensed CC-BY-4.0
Presentation file used in the Open source AI Tools for bioimage analysis workshop @ICOB, Academia Sinica, Taiwan (2024)Introduce ilastik, StarDist, Cellpose, Segment Anything Model (SAM), and how to use it briefly. Full video recording (in Chinese) is available on YouTube: https://youtu.be/KqwssouW0G0 This document is part III of the previous document:Chu, W.-C. (2024). Bioimage Analysis with FIJI /ImageJ & Friends workshop (2024) @ICOB, Academia Sinica, Taiwan. Zenodo. https://doi.org/10.5281/zenodo.12803966
data_visualization_tutorial#
Stefan Halfpap
Published 2025-04-25T21:00:39+00:00
Tags: Data Visualization
Content type: Github Repository
image-processing-basics#
Myles Scolnick
Published 2025-05-27T08:31:14+00:00
Licensed APACHE-2.0
Teaching material for image processing and analysis
Tags: Bioimage Analysis
Content type: Github Repository
qupath-workshop#
Antoine A. Ruzette, dependabot[bot]
Published 2025-01-16T14:05:02+00:00
Licensed CC-BY-4.0
Materials supporting the QuPath workshop at Harvard Medical School.
Tags: Notebook, Slides, Collection
Content type: Github Repository