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@CellMigrationLab

Cell Migration Lab

README.md

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.

About us

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 the Solution for Health research profile and INFLAMES Flagship. We are affiliated with Turku Bioscience Centre and use their core facilities for our research.

Latest Research

Discover our recent findings and publications: Research.

Software Projects

At the Cell Migration Lab, we develop, co-develop and contribute (in various ways) to various innovative software projects to analyze microscopy images. Below are some of the key software projects we have been involved with:

  • SReD: Structural Repetition Detector Plugin for ImageJ and Fiji GitHub
  • PhotoFiTT (2024): Phototoxicity Fitness Time Trial. A Quantitative Framework for Assessing Phototoxicity in Live-Cell. GitHub
  • CellTracksColab (2024): A platform for compiling, analyzing, and exploring tracking data. GitHub
  • NanoPyx (2024): A library for analyzing light microscopy and super-resolution data, successor to NanoJ. GitHub
  • DL4MicEverywhere (2024): An extension of ZeroCostDL4Mic featuring interactive Jupyter notebooks for bioimage analysis using deep learning. GitHub
  • eSRRF (2023): Provides super-resolution approach and optimal parameter prediction for super-resolution microscopy. GitHub
  • Fast4DReg (2023): A Fiji plugin for 2D and 3D video drift correction in all axes. GitHub
  • TrackMate (2022): Automated tracking software analyzing bioimages, distributed as a Fiji plugin. GitHub
  • ZeroCostDL4Mic (2021): Allows the use of popular deep-learning neural networks for tasks in bioimage analysis. GitHub
  • SRRF TFM (2020): Enhances the output of traction force microscopy using super-resolution microscopy. Read More
  • FiloMap (2019): ImageJ and R scripts for mapping protein localization within filopodia. GitHub
  • FiloQuant (2017): A Fiji plugin for automated detection and quantification of filopodia properties. GitHub

For more details on each project, visit our software page.

Open Data

At the Cell Migration Lab, we're committed to open science principles. When possible, our extensive research-based datasets are made publicly available to catalyze further scientific discovery and collaboration. These datasets cover diverse topics. Explore our datasets and contribute to the ongoing scientific dialogue. Visit our GitHub page for a comprehensive list of our open datasets.

If you are interested in our deep learning models and training datasets, check our Model Zoo.

Training

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

Join Us

Motivated students are always welcome to contact us!

Stay Connected

Visit our website for more insights, or follow us on Bluesky.

Contact Us

For software, dataset queries, or collaborations, please feel free to contact us.

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Popular repositories Loading

  1. CellTracksColab CellTracksColab Public

    A platform for compiling, analyzing, and exploring tracking data

    Jupyter Notebook 42 4

  2. Fast4DReg Fast4DReg Public

    Fast4DReg is a Fiji script for quick drift correction in time-lapse 3D-stacks. The script can be used to correct drift in all x-, y- and/or z-directions.

    Java 37 3

  3. Datasets Datasets Public

    List of openly available dataset generated by our lab

    9

  4. Plot-Stats Plot-Stats Public

    Jupiter notebooks created to help us plot and analyse our datasets

    Jupyter Notebook 4

  5. FiloMAP FiloMAP Public

    ImageJ and R scripts used to map the localisation of proteins whithin filopodia and generate filopodia maps.

    R 3

  6. I2K_2024 I2K_2024 Public

    I2K 2024 workshop materials for "Object Tracking and track analysis using TrackMate and CellTracksColab"

    3

Repositories

Showing 10 of 13 repositories
  • Plot-Stats Public

    Jupiter notebooks created to help us plot and analyse our datasets

    CellMigrationLab/Plot-Stats’s past year of commit activity
    Jupyter Notebook 4 MIT 0 1 0 Updated Nov 22, 2024
  • .github Public
    CellMigrationLab/.github’s past year of commit activity
    0 1 0 0 Updated Nov 11, 2024
  • I2K_2024 Public

    I2K 2024 workshop materials for "Object Tracking and track analysis using TrackMate and CellTracksColab"

    CellMigrationLab/I2K_2024’s past year of commit activity
    3 GPL-3.0 0 0 0 Updated Oct 29, 2024
  • CellTracksColab Public

    A platform for compiling, analyzing, and exploring tracking data

    CellMigrationLab/CellTracksColab’s past year of commit activity
    Jupyter Notebook 42 MIT 4 7 1 Updated Oct 28, 2024
  • Fast4DReg Public

    Fast4DReg is a Fiji script for quick drift correction in time-lapse 3D-stacks. The script can be used to correct drift in all x-, y- and/or z-directions.

    CellMigrationLab/Fast4DReg’s past year of commit activity
    Java 37 MIT 3 1 0 Updated Oct 25, 2024
  • PDAC_DL Public

    GitHub page associated with the publication "Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers"

    CellMigrationLab/PDAC_DL’s past year of commit activity
    Jupyter Notebook 2 GPL-3.0 0 0 0 Updated Oct 9, 2024
  • Datasets Public

    List of openly available dataset generated by our lab

    CellMigrationLab/Datasets’s past year of commit activity
    9 MIT 0 0 0 Updated Oct 4, 2024
  • AdhesionFlowSimulator Public

    AdhesionFlowSimulator models cell adhesion dynamics under flow, simulating interactions between cells and surfaces. It allows for the analysis of cell attachment across different flow speeds, adhesion strengths, and receptor patterns.

    CellMigrationLab/AdhesionFlowSimulator’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Oct 1, 2024
  • GithubToText Public

    Code to automatically copy a chosen Github repo into a text file

    CellMigrationLab/GithubToText’s past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Sep 2, 2024
  • Fiji_macros Public

    A small collection of useful macro for Fiji

    CellMigrationLab/Fiji_macros’s past year of commit activity
    ImageJ Macro 0 MIT 1 0 0 Updated Aug 27, 2024
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