Welcome to the GitHub repository of the Cell Migration Lab! Our lab is dedicated to understanding cell migration, focusing on cancer research. We also develop image analysis tools to advance this field.
The cell migration lab is located in Turku, Finland. The lab started in 2019 and is part of the Cell Biology department at Åbo Akademi University. We are part of Turku Bioscience Centre, the IMMENs Centre of Excellence and the INFLAMES Flagship.
Discover our recent findings and publications: Research.
- Mold for Zebrafish embryo (2025): Customizable FDM-based zebrafish embryo mold for live imaging GitHub
At the Cell Migration Lab, we develop, co-develop, and contribute to software for microscopy and image analysis.
- NucleiSky (2026): Image registration and ROI matching for microscopy images using nuclei constellations. Paper · GitHub
- LabConstrictor (2026): From Jupyter Notebook to Desktop App in One Click Paper · GitHub
- EZInput (2026): a Python library that simplifies the creation of graphical user interfaces Paper · GitHub
- SReD (2025): Structural Repetition Detector Plugin for ImageJ and Fiji Paper · GitHub
- Rxiv-Maker (2025): a toolbox that converts markdown into a publication-ready PDF Paper · GitHub
- PhotoFiTT (2024): Phototoxicity Fitness Time Trial. A Quantitative Framework for Assessing Phototoxicity in Live-Cells. Paper · GitHub
- NanoPyx (2024): A library for analyzing light microscopy and super-resolution data, successor to NanoJ. Paper · GitHub
- DL4MicEverywhere (2024): An extension of ZeroCostDL4Mic featuring interactive Jupyter notebooks for bioimage analysis using deep learning. Paper · GitHub
- CellTracksColab (2024): A platform for compiling, analyzing, and exploring tracking data. Paper · GitHub
- eSRRF (2023): Provides a super-resolution approach and optimal parameter prediction for super-resolution microscopy. Paper · GitHub
- Fast4DReg (2023): A Fiji plugin for 2D and 3D video drift correction in all axes. Paper · GitHub
- TrackMate (2022): Automated tracking software analyzing bioimages, distributed as a Fiji plugin. Paper · GitHub
- ZeroCostDL4Mic (2021): Allows the use of popular deep-learning neural networks for tasks in bioimage analysis. Paper · GitHub
- FiloMap (2019): ImageJ and R scripts for mapping protein localization within filopodia. Paper · GitHub
- FiloQuant (2017): A Fiji plugin for automated detection and quantification of filopodia properties. Paper · GitHub
- SRRF TFM (2020): Enhances the output of traction force microscopy using super-resolution microscopy. Paper
For more details on each project, visit our software page.
At the Cell Migration Lab, we're committed to open science principles. When possible, our research datasets are made publicly available to catalyse further scientific discovery and collaboration. Our open data collection currently lists 69 datasets. Browse them on our datasets page.
At the Cell Migration Lab, we also provide training in several topics in image analysis including tools developed in the lab. Here are some trainings provided:
Workshop in I2K 2024 "Object Tracking and Track Analysis using TrackMate and CellTracksColab"
Bioimage Analysis for Quantitative Microscopy course
Motivated students are always welcome to contact us! See how to join.
Visit our website for more insights, or follow us on Bluesky.
For software, dataset queries, or collaborations, please feel free to contact us.
