Published June 7, 2023 | Version V0
Lesson Open

BioImage Analysis and Superresolution Microscopy Workshop 2023 (at Dartmouth College)

  • 1. VMCF, Faculty of Science, Charles Univerity
  • 2. BioMT, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755 USA


Hosting institution:


  • 1. BioMT, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755 USA
  • 2. DFG Cluster of Excellence "Physics of Life", TU Dresden


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 and ThunderSTORM sample data

Date: June 6-7, 2023
Time: 9am - 5pm
Location: Dartmouth College, 74 College St, Hanover, Kellogg 200
Sponsor: bioMT (Lunch and coffee breaks)

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, 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.


The workshop was supported by bioMT through NIH NIGMS grant P20-GM113132, and Vinicna Microscopy Core Facility which is co-financed by the Czech-BioImaging large RI project LM2023050. Some of the results presented would not be possible without the project "e-Infrastruktura CZ" (e-INFRA LM2018140) provided within the program Projects of Large Research, Development and Innovations Infrastructures ,and "Transformace pro VŠ na UK, specifický cíl A, NPO_UK_MSMT-16602/2022" We used image set BBBC038v1, available from the Broad Bioimage Benchmark Collection [Caicedo et al., Nature Methods, 2019], available at


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