Robert Haase

Dr. rer. medic. Robert Haase

Lecturer, Training Coordinator
Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden/Leipzig
Universität Leipzig
Humboldtstraße 25
04105 Leipzig

Research interests

• Large language models for Bio-image Analysis
• GPU-accelerated image processing
• Software bridging bio-imaging and image data science
• Quantitative image analysis of tissues

Affiliations / organizations

• Center of Scalable Data Analytics and Artificial Intelligence (ScaDS.AI) Dresden / Leipzig, Leipzig University
• DFG Cluster of Excellence “Physics of Life” Technische Universität Dresden (PoL)
• Network of European BioImage Analysts (NEUBIAS)
• GloBIAS
• German Bioimaging (GerBI)
• NFDI4BioImage

Curriculum vitae

• Since 2023 Lecturer and Training Coordinator, Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), Leipzig University
• 2020-2023 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
  • Society for Knowledge Exchange in BioImage Analysis (2023-2025)

Open-Access Training Materials

• Bio-image Analysis Notebooks

2024

• ScaDS.AI Bio-image Data Science Training School, May 2024 (Website)

• DataWeek Leipzig (Session slides: git, Sharing/Licensing Data Management)

• Bio-image Data Science Lecture + Practicals, Summer Semester 2024, Leipzig University (Materials)

• Sharing and Licensing workshop, ScaDS.AI General Assembly, (Slides)

2023

• Prompt Engineering Tutorial (ScaDS.AI Living Lab) (Slides + Notebooks)

• Napari Tutorial (ScaDS.AI Life Science Jour Fixe) (Slides + Notebooks)

• Generative Artificial Intelligence for Bio-image Analysis (I2K2023 Tutorial) (Video, Slides)

• EMBO Practical Course on Advanced Methods of Bio-image Analysis, Heidelberg ( (Website, Video lecture 1, Slides 1, Video lecture 2, Slides 2))

• DIGS-BB Principles of Light Microscopy – Course for DIPP Students, Bio-image Analysis session, Dresden (Website, Materials)

• PoL Early Career Bio-Image Analysis Training School, Dresden (Website, Materials)

• PoL GPU-Accelerated Bio-Image Analysis Training School, Dresden (Website, Materials)

• Guest lecture in the master program Regenerative Biology and Medicine “Quantitative Bio-image Data Analysisin the age of Machine Learning” (Materials)

• NEUBIAS Pasteur course on Bioimage Analysis, Insitut Pasteur, Paris (Website, Materials)

• Latin America workshop on Image data science with Python and Napari, Virtual (Materials)

• 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

• Image data science with Python and Napari, virtually at EPFL Lausanne (Slides)

• 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)

• 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)

• 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)

• Tracking cells in microscopy image data, EMBO Course on 3D Developmental Imaging, IGC Oeiras (Website, Slides)

• Advanced bio-image analysis, image data science & AI, Workshop at Zebrafish PI Meeting, Dresden (Slides)

• Current challenges in GPU-accelerated image processing for the life sciences, Guest Lecture in High Performance Computing, TU Dresden (Slides)

2021

• 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)

• ImageJ Macro Programming, Centre for Cellular Imaging, Bio-image analysis Course, Gothenburg (Slides)

• Interactive Data Visualization 101 with Fiji & Friends, HIP Summer School (Slides)

• Object tracking in images, Seminar at HZDR Dresden (Slides)

• Quantitative Bio-image Analysis, DIGS-BB Course Principles of Light Microscopy (Slides)

• Sharing and licensing material, EMBO Workshop on Advanced Methods in Bio-image Analysis (Website, Slides)

• On-the-fly image processing with Python and napari, Smart Microscopy Workshop - Image analysis to improve remote image acquisition (Slides)

2020

• Applied Bio-Image Analysis, Lecture in Molecular Bioengineering (Master) and Molecular Biology and Biotechnology (Bachelor) at BIOTEC, TU Dresden (Videos, Slides)

• Designing GPU-accelerated Image Data Flow Graphs for CLIJ2 and clEsperanto, Images2Knowledge Workshop, 2020 (Video, Slides, Materials)

• GPU-accelerated Image Processing with CLIJ2, NEUBIAS Academy @Home (Video, Slides)

• Intelligent Systems for Bio-Image Analysis, Guest Lectures at Faculty of Computer Science, TU Dresden (Slides)

2019

• GPU-accelerated Image Processing in ImageJ Macro, NEUBIAS Training School 13 for Facility Staff, INESC TEC Porto (Website, Slides)

• Stitching & Image Registration, NEUBIAS Training School 12 for Early Career Scientists, INESC TEC Porto (Website, Slides)

• ImageJ Macro Programming & GPU-acceleration, Image Analysis Introductory Course, CCI University of Gothenbourg (Slides)

• Applied Bio-image analysis, Lecture part of Bioinformatics master programme, Charles University Praque (Slides)

• Applied Bio-image analysis, Lecture part of Molecular Bioengineering master programme at BIOTEC Dresden (Slides)

• 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

• Generative AI / LLMs:
  • bia-bob
  • Benchmarking LLMs for Bio-image Analysis
  • blablado
  • story-writer
  • darth-d
  • prompting-pptx
• stackview
• clesperanto
  • pyclesperanto_prototype
  • pyclesperanto
  • clesperantoj_prototype
• CLIJ
  • CLATLAB
  • clicy
  • clupath
• Accelerated pixel and object classification
  • apoc
  • napari-apoc
  • Fiji/CLIJx-apoc
• 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

• ORCID
• Google Scholar
• Github
• YouTube
• Twitter

Recent talks

• “Large Language Models for Bio-image Analysis” ScaDS.AI Summer School, June 24th 2024 (Website)

• “Cultivating Open Training to advance Bio-image Analysis”, FocalPlane Webinar, April 27th 2024 (Website)

• “Large Language Models for Bio-image Analysis”, ScaDS.AI Living Lab Lecture, April 4th 2024, (Video, Slides)

• “Prompt Engineering for Quantitative Bio-image Analysis”, Monash Advanced Microscopy Seminar (online), March 20th 2024, (Slides)
• “Bio-image Analysis with the Help of Large Language Models”, Leibnitz IPHT Semina, Jena, March 13th 2024 (Slides)

• “Bio-image Analysis using Large Language Models”, IMOL Seminar, Johann Wolfgang Goethe University Frankfurt am Main, March 6th 2024 (Website, Slides)

• “Cultivating Open Training”, SaxFDM Digital Kitchen, March 2024, (Website, Slides)
• “Cultivating Open Training”, Workshop on Efficiently Communicating Bio-image Analysis, Buxted Park, 12-15 Feb 2024, (Slides)
• “Nichts hält ewig – Wie gehen wir damit um?” (“Nothing is forever - How do we deal with that?”), 5. Ulmer Workshop “Administrative Herausforderungen in Core Facilities und Technologieplattformen”, Ulm University 2023 (Website, slides)
• “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)

• “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

• ImageJ Macro
• CLIJ – GPU accelerated image processing in ImageJ Macro

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)