BioImage Analysis and Data Processing Workshop 2025

BioImage Analysis and Data Processing Workshop 2025#

Date: June 30 – July 4, 2025
Location: Room B311 - VMCF Microscopy Facility, Vinicna 7, Prague, Czechia
Form: Hybrid form of presentations; hands-on sessions are in-person only
Time Zone: All times are in CEST (GMT+2)

Program at a Glance#

  • Day 1: Deconvolution and ThunderSTORM

  • Day 2: CellPose and TrackMate

  • Day 3: Napari

  • Day 4: mesoSPIM + Leica AIVIA

  • Day 5: Affordable microscopes based on 3D printing and smartphones + Bioimage analysis community

Full Program#

Day 1#

10:00 – 11:00
Registration (outside Room B332)
Optional: software installation on your own laptops

11:00 – 11:15
Welcome note from VMCF

  • Miroslav Hyliš, Ph.D.

  • Martin Schätz, Ph.D.

  • Zuzana Burdíková, Ph.D.

11:25 – 12:00
Introduction to super-resolution microscopy
Zuzana Burdíková, Ph.D.

  • Image Formation in Fluorescence Microscopy

  • Resolution and Noise

  • Single-molecule localization microscopy (STORM, PALM, DNA-PAINT, …)

  • Structured Illumination Microscopy (SIM)

12:00 – 13:20
Lunch

13:20 – 14:00
Deconvolution of optical microscopy images
Prof. Rainer Heintzmann, IPHT, Jena

14:00 – 14:10
Coffee break

14:10 – 14:50
Introduction to Image processing in FIJI, ImageJ
Karel Stepka, Ph.D.

  • Two-channel colocalization

  • p-Value of colocalization, data filtering

  • Quantitative analysis

  • Data visualization, 3D visualization

  • Image export 14:50 – 15:10
    Coffee break

15:10 – 15:50
ThunderSTORM software Introduction
Zdenek Svindrych, Ph.D.

  • Rationale and features 16:00 – 17:00
    ThunderSTORM software hands-on
    Zdenek Svindrych, Ph.D.

  • Installation

  • Processing 2D and 3D STORM datasets

Day 2#

10:00 – 12:00
CellPose

CellPose segmentation + Tracking

Day 3#

10:00 – 12:00
Napari Morning Session
Marcelo Leomil Zoccoler, Ph.D. (TU Dresden)

12:00 – 13:00
Lunch

13:00 – 16:00
Napari Afternoon Session
Marcelo Leomil Zoccoler, Ph.D. & Martin Schätz, Ph.D.

Day 4#

10:00 – 12:00
Benchtop mesoSPIM: open-source light-sheet microscope
Marco Garbelli, Ph.D.

  • Project introduction

  • Remote demo

  • Data visualization in Fiji/BigStitcher and 3DScript

12:00 – 13:00
Lunch

13:00 – 14:00
Introduction to AIVIA analysis from Leica Microsystems

  • AIVIA overview

  • LAS X + AIVIA Rare Events

  • Adaptive deconvolution

14:00 – 16:00
Hands-on session on AIVIA online

  • License installation

  • Demo data showcase

  • User data testing

Day 5#

10:00 – 11:00
Affordable microscopes based on 3D-printing and smartphones
Prof. Rainer Heintzmann, IPHT, Jena

11:00 – 11:30
Image analysis communities
Martin Schätz, Ph.D.

Contents