phase contrast cell tracking


I have worked mostly with Zernike's phase contrast imaging because it is readily compatible for all kinds of microfluidic chips, plastics, PDMS or glass. DIC has been used extensively by other groups but is very difficult touse DIC to image with plastic microfluidic chips.
However due the principle of the phase contrast, the phase difference was transferred into intensity difference. Halo artifacts are relieved somewhat by apodized phase contrast design but still quite intensive. Thus it is very difficult to perform automated cell segmentation using phase contrast images in comparison to fluorescence cell tracking.

There are several software packages developed throughout the world for phase contrast microscopy cell tracking.
I have tried many but most of them doesn't work perfectly for my data. 
This page servers as a information hub on the existing software out there available.

If there are more information you know that i missed on software for segmentation and tracking, please be so kind and let me know so we can keep this page as updated as possible.

Cell migration
  • chemotaxis
  • haptotaxis
  • mechanotaxis (durotaxis)
  • electrotaxis
  • rheotaxis
Review articles
 https://onlinelibrary.wiley.com/doi/pdf/10.1111/jmi.12184
https://www.cell.com/cell-systems/fulltext/S2405-4712(18)30241-2
https://www.sciencedirect.com/science/article/pii/S0962892415001658

Conventional computer vision

MATLAB

  1. (2008) uTrack, Prof. Danuser, UT southwestern
  2. (2009) DYNAMIK, Stefan Jaeger, MPI
    • https://academic.oup.com/bioinformatics/article/25/18/2383/196420
  3. (2009) Hand et al., MacNeil Lab, U Sheffield, J microscopy, 2009
  4. (2009) NeuronCyto, Yu Lab, BII Star, Singapore
  5. (2010) Ct3D, Mosig, Ruhr-Universitat Bochum, Germany
  6. (2010) Time Lapse Analyser, Uni-ulm, Germany
  7. (2011) MOSAIC, MPI-CBG, Germany (Previously ETH Zurich)
  8. (2011) Schnitzcells, Elowitz Group, Caltech
  9. (2011) cell2numbers
  10. (2012) Takeo Kanade Lab, CMU
  11. (2012) Directional gradient vector flow (DVGF) from Prof. Kinneret Keren, Technion Israel Institute of Technology
  12. (2012) TLM-Tracker, Technische Universitat Braunschweig, Germany
  13. (2012) Cell image velocimetry (CIV), Koumoutsakos, ETH Zurich
  14. (2013) CellSegm, Hodneland Group, U bergen, Norway
  15. (2013) PHANTAST, Szita group, UCL
  16. (2014) CellX, Stelling Lab, ETH Zurich
  17. (2014) EGT, Information Systems Groups, NIST
  18. (2014) FogBank, Information Systems Group, NIST
  19. (2014) TGMM, Amat et al., HHMI, US
  20. (2014) CellGeo, Elston, U North Carolina Chapel Hill
  21. (2014) ACTIVE, Manning & Henderson group, Syracuse U
  22. (2014) SpatTrack, Daniel Wuestner, U Southern Denmark
  23. (2015) Graph cut methods, Ronneberger Group, U Freiburg, Germany
  24. (2015) CellTracker, Horvath Group, Hungarian Academia of Sciences
  25. (2016) Omnisphero, Du & Mosig, Ruhr-Universitat Bochum, Germany
  26. (2016) Oufti, Yale university
  27. (2016) LEVER, Andrew Cohen Lab, Drexel U
    • (2016) CellMigrationTracking, saminaji, Ghent U
    • (2017) Cell cycle analysis, NIH
    • (2017) Multilevel classification, Essa Lab, Mansoura University
    • (2018) Loewke group, segmentation for QPM
    • (2018) Tractrac, U Rennes, France
    • (2018) fastTracks, NIH
    • (2018) MATLAB-Celltracking

    ImageJ plugins

    Python

    1. (2005) ivctrack - Oliver Debeir, ULB, Belgium
    2. (2017) https://github.com/SynBioUC/piv
    3. (2018) CellTracking, Heather Deter, South Dakota U
    4. (2018) Trackpy

    Self contained

    1. (2006) Starry Nite, Bao Group, U Washington
    2. (2008) CellTrack, Sacan Lab, Ohio State U
    3. (2013) iTrack4U (similar to ivctrack)
    4. (2013) CellMissy, Lennert Martins Lab, Ghent University
    5. (2013) Pathfinder, Liu Group, U Colorado 
    6. (2015) Cellprofiler tracker
      • https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0759-x
    7. (2015)Mouse Embryo tracking, Cicconet & Gunsalus, NYU
    8. (2015) Icy
    9. (2016) tTt and qTfy, Timm Schroeder group, ETH Zurich
    10. (2017) NucliTrack,
    11. (2017) MotilityLab, Miller lab, Washington U in st louis & Textor Lab, Radboud University, The Netherlands
    12. (2017) fastER, Timm Schroeder Group, ETH Zurich
    13. (2018) Microscopy Image Browser, U Helsinki, Finland

    Data analysis tool

    1. (2007) Celltool, cell-shape analysis software from Pincus lab in Stanford
    2. (2012) PERSIST, U Warwick, UK 
    3. (2013) Ibidi Cell migration tool 
    4. (2014) DiPer, Gorelik & Gautreau, LEBS, France
    5. (2016) Lineage Mapper, Information Systems Group, NIST
    6. (2017) Biotracks, Cell migration standardization organisation
    7. (2017) MigrationMiner, Tim Becker, Broad Institute
    8. (2017) CMP:Cell migration analysis platform
    9. (2018) Heteromotility, Jacob Kimmel, UCSF
    10. (2018) Cell-Migration-Analysis, Gaborski Lab

    Commercial

    1. Volocity PerkinElmer
    2. Imaris, Bitplane
    3. Metamorph, Molecular devices
    4. Cellomics, ThermoFisher
    5. IN Cell investigator, GE life sciences
    6. simi biocell

    Machine/Deep learning methods

    1. (2016) Deepcell, David Van Valen Caltech, (Previously @ Stanford)

    2. (2016) RADHicaL, Andrew Janowczyk, Case Western U,
    3. (2018) Lanternfish, Jacob Kimmel, Marshall Lab, UCSF
    4. (2018) Usiigaci, Hsieh-Fu Tsai, Shen Unit, OIST
    5. (2018) Hirohiko Niioka, Osaka U,
    6. (2018) Shinsuke Yuasa, Keio U,
    7. (2018) Saad Ullah Akram,
      1. https://github.com/SaadUllahAkram/CellTracker
      2. https://arxiv.org/pdf/1705.03386.pdf
    8. (2018) fnet, Gregory Johnson, Allen Institute
      1. https://www.nature.com/articles/s41592-018-0111-2
      2. https://www.allencell.org/label-free-determination.html
      3. https://github.com/AllenCellModeling/pytorch_fnet


    DIC

    1. (2013) Obara Lab, U Durham
      • https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-134
    2. https://www.ncbi.nlm.nih.gov/pubmed/20483698

    None-Phase contrast

    1. (2010) Cellcognition, Gerlich group, ETH Zurich
    2. (2011) cellTracer, West Group, Duke U,
    3. (2012) CellAnimation, Georgescu Lab, Vanderbilt U
    4. (2013) TACTICS tools box, Swinburne University of Technology, Australia
    5. (2014) Mother Machine analyzer, Gene Meyers Group, MPI-CBG
    6. (2015) ADAPT, Barry Lab, Francis Crick Institute, UK
    7. (2016) 3D cell tracking of zebrafish, Juliane Liepe, MPI
    8. (2017) FlowcatchR, Marini, U Mainz, Germany

    Computer vision resources

    1. Peter's function of matlab and octave for image processing
    2. mohotas library for image processing
    3. Cellmodeller
    4. DIPlib, Prof. Bernd Rieger, TU Delft