haesleinhuepf.github.io
Robert Haase
Dr. rer. medic. Robert Haase Group Leader Bio-image Analysis Technology Development Group DFG Cluster of Excellence “Physics of Life” Technische Universität Dresden Arnoldstrasse 18 01307 Dresden
Research interests
- Bio-image Analysis Technology Development for understanding the Physics of Life
- Software bridging bio-imaging and image data science
- GPU-accelerated image processing
- Quantitative image analysis of tissues
Affiliations / organizations
- DFG Cluster of Excellence “Physics of Life” Technische Universität Dresden (PoL)
- Center for Systems Biology Dresden (CSBD)
- Network of European BioImage Analysts (NEUBIAS)
- German Bioimaging (GerBI)
- NFDI4BioImage
Curriculum vitae
- Since 2020 Group Leader, Bio-image Analysis Technology Development Group, DFG Cluster of Excellence “Physics of Life”, University of Technology, TU Dresden
- 2017-2020 Postdoctoral researcher, Gene Myers lab, Max Planck Insitute for Molecular Cell Biology and Genetics Dresden / Center for Systems Biology Dresden
- 2015-2017 Bio-Image Analyst, Scientific Computing Facility, Max Planck Insitute for Molecular Cell Biology and Genetics Dresden / Scionics GmbH
- 2013-2015 Scientific Assistant, High-Precision Radiotherapy Group (Dr. Perrin / Dr. Richter), OncoRay, Medical Faculty Carl Gustav Carus, University of Technology, TU Dresden
- 2010-2013 PhD Student, Scientific Assistant, Biological and Molecular Imaging Group (Prof. Abolmaali), OncoRay, Medical Faculty Carl Gustav Carus, University of Technology, TU Dresden
- 2008-2010 Student Assistant, Biological and Molecular Imaging Group (Prof. Abolmaali), OncoRay, Medical Faculty Carl Gustav Carus, University of Technology, TU Dresden
- 2006-2010 Student of Computer Science, University of Applied Sciences, HTW Dresden
- 2004-2005 Junior IT Project Leader, Spiritlink GmbH, Erlangen
- 2001-2004 Trainee, IT specialist for software development (Fachinformatiker Fachrichtung Anwendungsentwicklung), Spiritlink GmbH, Erlangen
Funding
- CZI Essential Open Source Software program
- GPU-accelerating Fiji and Friends Using Distributed CLIJ, NEUBIAS-style (2021-2024), collaboration with Stephane Rigaud (Insitut Pasteur, France) and Martin Jones, Amy Strange and Lucy Collinson (The Francis Crick Institute, London, UK)
- CZI Napari Plugin grants
- Improving Image Processing (2021-2022), collaboration with Lachlan Whitehead (WEHI Australia)
- Seamless Integration of Quantitative Bio-Image Analysis Plugins (2022-2023)
- DFG National Research Data Management Initiative
- NFDI4BioImage (2023-2028), lead by Stefanie Weidtkamp-Peters, Heinrich Heine University Düsseldorf
- ANR-DFG French-German Collaboration for Joint Projects in Natural, Life and Engineering Sciences
- DeepLineage project (2022-2025) lead by Michalis Averof (IGFL Lyon, France)
- BMBF Program for Interdisciplinary Collaborations to investigate Pathomechanims
- PACETherapy project (2022-2025) lead by Mike O Karl, DZNE/TU Dresden
- CZI Advancing Imaging Through Collaborative Projects
Open-Access Teaching Materials
2023
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EMBO Practical Course on Advanced Methods of Bio-image Analysis, Heidelberg ( Website, Video lecture 1, Slides 1 Video lecture 2, Slides 2)
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DIGS-BB Principles of Light Microscopy – Course for DIPP Students, Bio-image Analysis session, Dresden (Website, Materials)
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PoL Early Career Bio-Image Analysis Training School, Dresden (Website, Materials)
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PoL GPU-Accelerated Bio-Image Analysis Training School, Dresden (Website, Materials)
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NEUBIAS Pasteur course on Bioimage Analysis, Insitut Pasteur, Paris (Website, Materials)
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Latin America workshop on Image data science with Python and Napari, Virtual (Materials)
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Bio-Image Analysis, Biostatistics, Programming and Machine Learning for Computational Biology Lecture in Molecular Bioengineering (Master) and Molecular Biology and Biotechnology (Bachelor) at CMCB, TU Dresden (Materials)
2022
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Image data science with Python and Napari, virtually at EPFL Lausanne (Slides)
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Bio-Image Analysis, Biostatistics, Programming and Machine Learning for Computational Biology Lecture in Molecular Bioengineering (Master) and Molecular Biology and Biotechnology (Bachelor) at CMCB, TU Dresden (Materials)
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Customizing ImageJ/Fiji using ImageJ Macro + Interactive Design of GPU-accelerated Image Data Flow Graphs in Fiji, Workshop Image analysis and data processing in the super-resolution microscopy, Faculty of Science, Charles University Prague (Slides)
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3D Image Data Science with open tools & CLIJ crash course: GPU-accelerated image processing in Fiji, EMBO Practical Course on Lightsheet Microscopy, CEITEC BRNO (Website, Slides, Slides, Slides)
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Tracking cells in microscopy image data, EMBO Course on 3D Developmental Imaging, IGC Oeiras (Website, Slides)
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Advanced bio-image analysis, image data science & AI, Workshop at Zebrafish PI Meeting, Dresden (Slides)
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Current challenges in GPU-accelerated image processing for the life sciences, Guest Lecture in High Performance Computing, TU Dresden (Slides)
2021
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Bio-Image Analysis, Biostatistics, Programming and Machine Learning for Computational Biology Lecture in Molecular Bioengineering (Master) and Molecular Biology and Biotechnology (Bachelor) at CMCB, TU Dresden (Materials)
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ImageJ Macro Programming, Centre for Cellular Imaging, Bio-image analysis Course, Gothenburg (Slides)
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Interactive Data Visualization 101 with Fiji & Friends, HIP Summer School (Slides)
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Object tracking in images, Seminar at HZDR Dresden (Slides)
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Quantitative Bio-image Analysis, DIGS-BB Course Principles of Light Microscopy (Slides)
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Sharing and licensing material, EMBO Workshop on Advanced Methods in Bio-image Analysis (Website, Slides)
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On-the-fly image processing with Python and napari, Smart Microscopy Workshop - Image analysis to improve remote image acquisition (Slides)
2020
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Applied Bio-Image Analysis, Lecture in Molecular Bioengineering (Master) and Molecular Biology and Biotechnology (Bachelor) at BIOTEC, TU Dresden (Videos, Slides)
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Designing GPU-accelerated Image Data Flow Graphs for CLIJ2 and clEsperanto, Images2Knowledge Workshop, 2020 (Video, Slides, Materials)
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GPU-accelerated Image Processing with CLIJ2, NEUBIAS Academy @Home (Video, Slides)
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Intelligent Systems for Bio-Image Analysis, Guest Lectures at Faculty of Computer Science, TU Dresden (Slides)
2019
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GPU-accelerated Image Processing in ImageJ Macro, NEUBIAS Training School 13 for Facility Staff, INESC TEC Porto (Website, Slides)
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Stitching & Image Registration, NEUBIAS Training School 12 for Early Career Scientists, INESC TEC Porto (Website, Slides)
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ImageJ Macro Programming & GPU-acceleration, Image Analysis Introductory Course, CCI University of Gothenbourg (Slides)
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Applied Bio-image analysis, Lecture part of Bioinformatics master programme, Charles University Praque (Slides)
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Applied Bio-image analysis, Lecture part of Molecular Bioengineering master programme at BIOTEC Dresden (Slides)
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Multiview Registration with Fiji and Tracking with Trackmate and Mastodon, NEUBIAS Training School 10 for Early Career Scientists, University of Luxembourg (Website, Slides, Slides)
2018
- Working with Pixels and Objects in 2D and 3D, NEUBIAS Training School 8 for Early Career Scientists, University of Edinburg (Website, Slides, Slides)
2017
- Introduction to ImageJ macro programming, Scientific Computing Facility, MPI CBG Dresden (Website, Slides)
2016
- Introduction to Image Analysis with Fiji, Scientific Computing Facility, MPI CBG Dresden (Website, Website, Slides)
Open Source Software
- CLIJ
- clesperanto
- Accelerated pixel and object classification
- stackview
- bia-bob
- Napari-plugins
- devbio-napari
- napari-segment-blobs-and-things-with-membranes
- napari-simpleitk-image-processing
- napari-pyclesperanto-assistant
- napari-cupy-image-processing
- napari-clusters-plotter
- napari-skimage-regionprops
- the-segmentation-game
- napari-curtain
- napari-assistant
- napari-process-points-and-surfaces
- napari-workflow-inspector
- napari-workflow-optimizer
- napari-script-editor
- napari-owncloud
- natari
- …
Publications
Recent talks
- “Challenges and opportunities for bio-image analysis core-facilities”, Danish BioImaging Stakeholder Meeting, 2023 (slides)
- “Current challenges in GPU-accelerated image processing for the life sciences”, Guest Lecture in Highly Parallel Computing, Faculty of Computer Sience, TU Dresden 2023 (slides)
- “User-friendly, interactive Bio-image Analysis Workflow Design in Napari”, The Crick Bio-image Analysis Symposium, London UK 2022 (slides)
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“Parallelization and heterogeneous computing: from pure CPU to GPU-accelerated image processing”, NEUBIAS Defragmentation Training School, 2022 (slides)
- “Hitchhiking through a diverse Bio-image Analysis Software Universe”, Frontiers in Bioimaging, Birmingham, UK 2022, (slides)
- “Advanced bio-image analysis, image data science & AI”, Zebrafish PI Meeting, Dresden, 2022 (slides)
- “Bio-image analysis island hopping: From Fiji to Napari and back”, talk at Instituto Gulbenkian de Ciência Oeiras, Portugal 2022 (slides)
- “clesperanto: Open-source, GPU-accelerated image processing across programming languages and software ecosystems” SIMposium 2022 (slides)
- “Current challenges in GPU-accelerated image processing for the life sciences”, Guest Lecture in Highly Parallel Computing, Faculty of Computer Sience, TU Dresden 2022 (slides)
- “GPU-accelerated bio-image analysis focusing on processing segmented images”, LS2 Switzerland Webinar 2021 (slides)
- “User friendly GPU-accelerated bio-image analysis beyond cell segmentation”, PSB Symposium Frontiers in Bioimaging, 2021 (slides)
- “Bio-image analysis island hopping: From Fiji to Napari and back”, EuroBioImaging Virtual Pub 2021 (slides, video)
- “Interactive image data flow graphs and GPU-accelerated image processing for everyone”, ABRF Annual Meeting 2021 (slides)
- “GPU Accelerated Image Processing with CLIJ2”, NEUBIAS Academy 2020 (slides, video)
Blog posts
- If you license it, it’ll be harder to steal it. Why we should license our work
- Sharing research data with Zenodo
- Scientific Data Analysis: User Documentation 101
- Managing Scientific Python environments using Conda, Mamba and friends
- Explorative image data science with napari
- Collaborative bio-image analysis script editing with git
- How CLIJ2 can make your bio-image analysis workflows incredibly fast
- Installing Microsoft buildtools on Windows
- Using StarDist in napari with GPU-support in Windows
- GPU-accelerated image processing using cupy and cucim
- Browsing the Open Microscopy Image Data Resource with Python
- GPU-accelerated image processing in the cloud using Google Colab and clEsperanto
Cheat Sheets
Data
- Tribolium castaneum embryo development as seen with lightsheet microscopy (“Lund” sample, first 36h)
- Example data for using napari-pyclesperanto-assistant
- Strausberg_Tribolium_LA-GFP_tailpole_run
- Example Data for clesperanto
- Napari plugin download statistics
- Awesome napari-plugins that are not on the napari-hub (yet)