Description and features:
This package able the automatic analysis of TFM data in time lapse with:
  • 1 to 2 beads channels(i.e. with two different beads colors)
  • 1 to 3 cells channels(for example with Bright Field, GFP and Hoechst channels)
  • multi-positions (i.e. several cells within a given experiment)
  • calculation of the traction forces
  • automatic cells segmentation carried out from their BF images
  • integration of the forces over the cells
  • tracking of the beads
  • focal adhesion segmentations
  • calculation of the traction forces applied on the focal adhesions
  • batch-processing using jobs creation, launching and tracking


As examples, following are videos obtained with the package:

Video1 - Example of time-lapse traction force analysis on a single cell

Fluorescence images of the beads with the bright-field images of the cells
           
In manual selection drag the mouse over the graph to browse all the movie images or change the movie speed
                       





Multi cell time-lapse traction force analysis




Drag the mouse over the graph to see each force value over time

Force vs time






Force ratio vs time













Video2 - Cell migration and mitosis







Video3 - Wound healing









To use the package, a job has to be defined through a GUI (Graphical User Interface):



Create_job_GUI Debug Data Folder Sequence images Reference images Number of acquired cells Slices Frames Frames begin Beads1 Beads2 Ch1 Ch2 Ch3 Number of Ch Kurto1 Kurto2 Kurto3 Young's modulus Precision_for_the_Regularization_factor_calculation Cells images Cells starting folder Cells ending folder image chosen from slices Beads reference images Beads reference starting folder Beads reference ending folder Beads reference images find focused slices Beads sequence images Beads sequence starting folder Beads sequence ending folder Beads sequence images find focused slices Traction force Traction starting folder Traction ending folder Traction force alignment Alignment make Alignment crop Traction force calculation PIV calculation Lambda calculation Force calculation Force superposition Cells analysis Cells analysis starting folder Cells analysis ending folder Cells selection Cells segmentation Force integration Traction high force Traction high starting folder Traction high ending folder Traction high enhance contrast High PIV calculation Particle tracker FA segmentation FA segmentation starting folder FA segmentation ending folder Traction force applied on FA Traction force applied on FA starting folder Traction force applied on FA ending folder Generate file and Exit Cancel Output_files_GUI Output Data Folder Output Sequence images Output Reference images Output Cells images Output Beads reference images Output Beads sequence images Output Traction force Output Traction force alignment Output Alignment make Output Alignment crop Output Traction force calculation Output PIV calculation Output lambda calculation Output Force calculation Output Force superposition Output Cells analysis Output Cells selection Output Cells segmentation Output Force integration Output Traction high force Output High PIV calculation Output Particle tracker Output FA segmentation Output Traction force applied on FA Output Generate file and Exit Cancel
Create_job_GUI_tooltip

Drag the mouse over the GUI to display tooltips corresponding to the help elements of the GUI window and a left click to open the help within a side page.

Use the slider buttons to move over the "JEasyTFM - Output files" window

Create_job_GUI_tooltip

Once defined, the job can then be launched:




The JEasyTFM version details as well as user manual can be reahed from the ImageJ Help>About_plugins> menu:




Which will then display the following window:



Authors:
 Philippe Carl (maintainer), UMR 7021 CNRS/Unistra, Illkirch, France
Philippe Rondé                 , UMR 7021 CNRS/Unistra, Illkirch, France


History:
 2020/07/31 - Version 1.0: First released version - The analysis package is made available for the community.
2023/01/23 - Version 2.0: Extension of the code to allow the calculation of the traction forces applied on the focal adhesions.
2023/01/23 - Version 2.1: For the particle_tracker feature JEasyTFM uses now an extension of the 1.0.25 version of the MosaicSuite code that had been released on 20 September 2022by the MOSAIC group.
            (instead of the 1.5. version of the Particle_Tracker code released September 2006)
2023/06/18 - Version 2.2: Addition of tooltips within the Create_job window (the addition of this feature required the 1.54f11 update of ImageJ).


Examples for evaluation:
 All the original raw microscopy images used for the Video1 and the Force vs time and Force ratio vs time plots can be downloaded from the following depositary submitted to curation:
 https://doi.org/10.57745/VAQNU8
171207_-_FAK--_-_FAK_-_GFP
171207_-_FAK--_-_FAK_-_GFP_-_Reference
180328_-_FAK--_-_FAK_-_GFP
180328_-_FAK--_-_FAK_-_GFP_-_Reference
180329_-_FAK--_-_FAK_-_GFP
180329_-_FAK--_-_FAK_-_GFP_-_Reference
These data can be analyzed up to the Force_superposition, Force_integration or Particle_tracker steps.


Source:
 Contained in the JAR file. To open a JAR file, change the extension from ".jar" to ".zip" and double click on it.
or
Download the create_job.java and launch_job.java files.


Installation:
 Fully functional bundle: To use the fully functional ImageJ bundle, just download the platform-dependent version of ImageJ bundled with Java file and containing all the tools needed for the package embedded:
 
  • ImageJ bundled with Java 8 and JEasyTFM under 64-bit Windows
    		•  ( 80.6 Mb)
     
  • ImageJ bundled with Java 8 and JEasyTFM under 64-bit Linux
    		•  ( 79.6 Mb)
     
  • ImageJ bundled with Java 8 and JEasyTFM under 64-bit Mac
    		•  (120 Mb)
     
  • ImageJ bundled with Zulu OpenJDK 13.0.6. and JEasyTFM under 64-bit Mac
    		•  ( 88 Mb)
    By unzipping and launching ImageJ, there will a JEasyTFM command at the right of the ImageJ menu for using it.
    ImageJ window

    or


    Manual installation: Proceed with the manual installation by downloading the ImageJ software and unziping it.
    Check wether the given ImageJ version is 1.54f11 or higher and if not replace the ij.jar file with its daily-build version.

    Download JEasy_TFM.jar to the plugins/jars folder, restart ImageJ, and there will a JEasyTFM new command at the right of the ImageJ menu.
    But in order to be fully fonctional, the JEasyTFM package uses several third party open source plugins which origin will be indicated next to the needed tool.
    Nevertheless, most of the linked plugins have been modified (with at least the the addition of some "direct static methods") and very often improved with the addition of new functionalities and features.
    All the modified source codes are available inside the jar files for further editing and improvements.
    Thus the following additional tools need to be downloaded from the links below (and not the original sites) to the plugins/jars folder:
     
  • the Particle Tracker PIV and Trajectories Inputs
    		•  plugin which is an improved version of the ParticleTracker_2D plugin from the MOSAIC group at the Systems Biology Dresden (CSBD).
     
  • the MosaicSuite-1.0.25_Full_extended
    		•  package which is an improved version of the MosaicSuite 1.0.25 package from the MOSAIC group at the Systems Biology Dresden (CSBD),
     
  • the Extended Depth of Field
    		•  plugin from the Biomedical Imaging Group at EPFL,
     
  • the Template Matching and Slice Alignment
    		•  plugin from the Qingzong Tseng website,
     
  • the Find Focused Slices
    		•  plugin from the Qingzong Tseng website,
     
  • the PIV (Particle Image Velocimetry)
    		•  plugin from the Qingzong Tseng website,
     
  • the Traction Force Microscopy
    		•  plugin from the Qingzong Tseng website,
     
  • the Apache Commons Mathematics
    		•  library file,
     
  • some of the previous plugins require the javacv
    		•  library files: javacv.jar, javacpp.jar, opencv.jar.

    Alternatively the download of all the previously described files can simply be replaced by downloading the JEasyTFM_files file and unzip it in the plugins/jars folder.

    Finally one of the platform-dependent library files need to be downloaded into the plugins/jars folder:
     
  • 32-bit Windows
    		•
     
  • 64-bit Windows
    		•
     
  • 64-bit Mac
    		•
     
  • 32-bit Linux
    		•
     
  • 64-bit Linux
    		•


    Quick evaluation and testing:
    		 Download example pictures (3.1 Gb) packed in a zip file with the temporal and reference images already saved into an ad hoc folder.
    or
    Download  the EPI    and beads    (i.e temporal) images ( 1.8 Gb ) into a folder (for example) named "My_folder"
    Along with the EPI_begin and beads_begin (i.e reference) images (38.5 Mb) into a folder (following)  named "My_folder_-_Reference"

    Install the JEasyTFM package either through the Fully functional bundle or Manual installation as described within the Installation paragraph.

    Start ImageJ, launch the plugin by clicking the JEasyTFM>Create_job menu element and the following JEasyTFM - Create job window will then be displayed.

    Perform a Drag&Drop of your previously created "My_folder" folder within the Data_folder text field which will automatically fill out the Data_folder, Sequence_images and Reference_images text fields.

    Your obtained JEasyTFM - Create job window configuration is then saved by pressing the Generate_file_and_Exit button and the analysis can be launched by clicking the JEasyTFM>Launch_job menu element.


    User documentations:
    		 The JEasyTFM_-_User_manual, JEasyTFM_-_Input_and_output_files_and_folders_names_and_format and JEasyTFM_-_Technical_requirements can be visualized online.
    Or download the JEasyTFM_-_User_manual for a complete description of the package
    and the JEasyTFM_-_Input_and_output_files_and_folders_names_and_format for a description of the input and output files and formats requirements.


    Reference:
    		 Philippe Carl, Philippe Rondé
    JEasyTFM: an open-source software package for the analysis of large 2D TFM data within ImageJ
    Bioinformatics Advances 2023, Volume 3, Issue 1, vbad156. https://doi.org/10.1093/bioadv/vbad156.


    Papers using the software:
    		 Durand, M.; Lelievre, E.; Chateau, A.; Berquand, A.; Laurent, G.; Carl, P.; Roux, S.; Chazee, L.; Bazzi, R.; Eghiaian, F.; Jubreaux, J.; Ronde, P.; Barberi-Heyob, M.; Chastagner, P.; Devy, J.; Pinel, S.
    The detrimental invasiveness of glioma cells controlled by gadolinium chelate-coated gold nanoparticles.
    Nanoscale 2021, 13 (20), 9236–9251. https://doi.org/10.1039/d0nr08936b.


    Webinar:
    		 A webinar on how to use the plugin can be seen here:



































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