Robert Haase

Dr. rer. medic. Robert Haase

Lecturer, Training Coordinator
ScaDS.AI Dresden/Leipzig
Data Science Center
Universität Leipzig
Humboldtstraße 25
04105 Leipzig

Research interests

Affiliations / organizations

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

2024

“Bio-image Analysis Code Generation”, From Images to Knowledge (I2K) virtual conference, Octoboer 2024 (Website)
“Large Language Models – an introduction for life scientists”, GloBIAS Seminar Series, Virtual, August 2024 (Slides, Website)
“ChatGPT for image Analysis” session in the “AI in Microscopy” Workshop, Virtual / Copenhagen Denmark, August 2024 (Slides, Website)
Bio-image Data Science Lecture + Practicals, Summer Semester 2024, Leipzig University (Materials, Slides)
“Large Language Models for Bio-image Analysis”, Mexican Bioimaging worshop (virtual), June 2024 (Website, Slides)
“Large Language Models for Quantiative Bio-image Analysis”, ScaDS.AI Summer School, Leipig June 2024 (Website, Slides)
Python Programming Basics, Leipzig University / Academic Lab / ScaDS.AI, June 2024 ([Website)
ScaDS.AI Bio-image Data Science Training School, May 2024 (Website)
Research Data & Software Management, DataWeek Leipzig (Session slides: git, Sharing/Licensing Data Management)
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:
stackview
clesperanto
CLIJ
- CLATLAB
- clicy
- clupath
Accelerated pixel and object classification
Napari-plugins

Publications

Recent talks

“Bio-Image Analysis Code Generation”, invited talk at “International Symposium on Image-based Systems Biology”, September 26th 2024, Jena (Website)
“GloBIAS - a global Society of Bio-Image Analysts”, Leipzig Research Data Forum, Sept 23rd 2024 (Website)
“Towards Preservation of Life Science Data with NFDI4BIOIMAGE” at NFDI4Microbiota Digital Preservation Workshop, September 3rd 2024 (Slides, Website)
“Large Language Models for Bio-image Analysis”, Biological Image Processing and Analysis Symposium, June 14th 2024, Nice France, (Slides, Website)
“Large Language Models for Scientific Image Analysis” at Networking event “From Distributed Data to Large AI Models” with Sächsische Staatskanzlei, May 30th Dresden, (Website)
“Large Language Models for Bio-image Analysis” at “HPC-Statuskonferenz 2024”, April 26th 2024, (Website)
“Prompt Engineering” at the Networking Event “AI at Leipzig University”, May 2024 (Slides)
“Research Software Management using git and zenodo” at RDM Symposium “From Papers to Pixels” at TU Dresden, May 27th 2024 (Slides, Website)
“Cultivating Open Training to advance Bio-image Analysis”, FocalPlane Webinar, April 27th 2024 (Slides, 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, Video recording)
“Bio-image Analysis with the Help of Large Language Models”, Leibnitz IPHT Seminar, 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)

Robert Haase

Research interests

Affiliations / organizations

Curriculum vitae

Funding

Open-Access Training Materials

2024

2023

2022

2021

2020

2019

2018

2017

2016

Open Source Software

Publications

Recent talks

Blog posts

Cheat Sheets

Data