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plugin:analysis:distance_analysis_diana_2d_3d:start [2019/01/17 10:37]
plugin:analysis:distance_analysis_diana_2d_3d:start [2019/05/14 08:18]
gilles [Author]
Line 1: Line 1:
 +===== Distance Analysis (DiAna) =====
  
 +This plugin allows :
 +  * Calculating co-localization between objects in 3D
 +  * Measuring 3D distances between nearest object, co-localized or not
 +  * Getting some 3D measurements about each objects
 +
 +The plugin can be used with labelled images, but it also integrates tools for the segmentation of the objects.
 +===== Author =====
 +
 +
 +Jean-Francois Gilles, Institute of Biology Paris Seine (France). jean-francois.gilles at upmc.fr
 +
 +Thomas Boudier ​ {{:​plugin:​stacks:​3d_ij_suite:​email.png|email}},​ [[https://​www.wehi.edu.au/​|Walter & Eliza Hall Institute]],​ Melbourne, Australia.
 +===== Features =====
 +
 +__Denoise filter__
 +  * Mean, Median, Gaussian blur filters
 +
 +__Segmentation of the objects__
 +  * Global thresholding
 +  * [[plugin:​segmentation:​3d_spots_segmentation:​start|3D spot segmentation]]
 +  * [[plugin:​segmentation:​3d_spots_segmentation:​start|3D iterative segmentation]]
 +
 +__Object based co-localization and distance analysis__
 +  * Colocalization from objects in image A, B, and/or A+B
 +  * Distance center – center ;
 +  * Distance center – edge ;
 +  * Distance edge – center ;
 +  * Surface in contact
 +  * Generates results representations such as:
 +  *       - Objects'​ map;
 +  *       - Colocalization object'​s map ;
 +
 +__Counting and measurements on objects__
 +
 +Counts the number of 3D objects in two stacks.
 +
 +Quantifies for each found object the following parameters:
 +  * Volume
 +  * Mean of the gray values
 +  * Surface area
 +  * Standard deviation of the gray values
 +  * Minimum & Maximum gray values
 +  * Centroid
 +  * Centre of mass
 +  * Feret'​s Diameter
 +
 +
 +===== Description =====
 +//
 +Note that when the mouse arrow passes on the items of the plugin, an explanation of each parameter is given//.
 +
 +Open at least two images. This plugin does not support RGB and 32-bits images.
 +
 +==== Images to analyse ====
 +Select the image A and the image B. The image A is the reference image.
 +
 +__Binary images:__
 +
 +Apply threshold with value 1
 +
 +Filter objects by size and remove objects from image edges is possible
 +
 +__Gray level images:__
 +
 +Apply filter to suppress noise (optional)
 +
 +Segment the image with either threshold or spot segmentation method
 +
 +- Threshold method :
 +
 +choose a threshold value
 +
 +Filter objects by size and remove objects from image edges is possible
 +
 +- Spot segmentation method : a tutorial for this method is found [[plugin:​segmentation:​3d_spots_segmentation:​start|here]] 
 +
 +- Iterative segmentation method : a tutorial for this method is found [[plugin:​segmentation:​3d_spots_segmentation:​start|here]]
 +
 +- Filter objects by size is possible
 +
 +
 +==== Interactions filters ====
 +
 +When unchecking « All objects touching » , the plugin will analyse the non co-localizing objects in addition to co-localizing objects.
 +
 +
 +==== Measures & Analysis ====
 +
 +__Colocalisation__
 +
 +Choose the parameters that will be measured for co-localizing objects
 +
 +__Distance__
 +
 +Choose the parameters that will be measured for non co-localizing objects
 +
 +__Shuffle__
 +
 +Select to do a shuffle of the objects on all the image or inside a mask
 +
 +__Other measures__
 +
 +Choose the parameters that will be measured for each objects
 +
 +__Resolution infos__
 +Image calibration has to be given for the measurements to be calibrated (otherwise they will given in pixels). If images opened are already calibrated, the plugin reads the calibration.
 +
 +
 +====The plugin retrieves :​====
 +
 +  * Objects from image A and B are listed in a ROI Manager.
 +  * Number of objects and number of co-localizing objects are given in the log window.
 +  * ColocResults gives measurements on co-localizing objects.
 +  * DistanceResults gives measurements on non co-localizing objects.
 +  * Curve of the shuffle (cumulative distances)
 +  * OtherMeasuresResults-A/​B gives measurements on each objects from images A and B.
 +
 +====Batch :====
 +if the recorder has a problem, here are some examples of macro line:
 +  * run("​DiAna_Segment",​ "​img=imageName.tif filter=median rad=1.0 thr=739-3-2000-true-false"​);​
 +  * run("​DiAna_Segment",​ "​img=C0.tif peaks=2.0-2.0-50.0 spots=30-10-1.5-3-2000-true"​);​
 +  * run("​DiAna_Segment",​ "​img=C0.tif iter=3-2000-20-30-true"​);​
 +  * run("​DiAna_Analyse",​ "​img1=imageA.tif img2=imageB.tif lab1=segA.tif lab2=segB.tif coloc distc=50.0 adja kclosest=1 dista=50.0 measure"​);​
 +===== Installation =====
 +
 +Download and copy the following jar in your plugins folder {{:​plugin:​analysis:​distance_analysis_diana_2d_3d:​diana_1.44.jar|diAna_1.44.jar}}
 +
 +Note that this version works only with {{:​plugin:​stacks:​3d_ij_suite:​mcib3d-core3.94.jar|}} and upper!
 +
 +You have also to manually download and copy into your plugins directory the [[plugin:​stacks:​3d_ij_suite:​start|3D ImageJ Suite]].
 +
 +If a problem appends, use version Core library : {{:​plugin:​stacks:​3d_ij_suite:​mcib3d-core3.94.jar|}} of mcib-core from the 3D Suite.
 +
 +
 +===== Citation =====
 +
 +Gilles J-F, Dos Santos M, Boudier T, Bolte S, Heck N. DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis. Methods 2016 Nov 24.  [[http://​www.sciencedirect.com/​science/​article/​pii/​S1046202316304649]]
 +
 +The spot segmentation method is based on :
 +Heck N, Dos Santos M, Amairi B, Salery M, Besnard A, Herzog E, Boudier T, Vanhoutte P, Caboche J. A new automated 3D detection of synaptic contacts reveals the formation of cortico-striatal synapses upon cocaine treatment in vivo. Brain Struct Funct. 2014 Jul 8. DOI 10.1007/​s00429-014-0837-2. ​     [[http://​link.springer.com/​article/​10.1007%2Fs00429-014-0837-2]]
 +===== License =====
 +
 +GPL distribution (see [[http://​www.cecill.info/​index.en.html|licence]] ). Sources for plugins are available freely.
 +
 +===== Change log =====
 +
 +  * 14/12/2016 v1.0.1: bug fixed for retrieving the calibration,​ add "​about"​ button
 +  * 16/12/2016 v1.1: add save 3D-ROIs button
 +  * 05/09/2017 v1.2: many improvements within the code. update possibility when initializing images in Analyse. macro enable for the labelling part
 +  * 25/01/2018 v1.3: 8bits bug fixed, add macro features
 +  * 05/07/2018 v1.4: bugs fixed
 +  * 19/12/2018 v.1.41: bugs fixed
 +  * 21/12/2018 v.1.42: show again info in the log
 +  * 17/01/2019 v.1.43: correct user interface and a bug with 2D images, thanks to Chin-Chun
 +  * 14/05/2019 v.1.44: bugs fixed and compatibility with the last version of 3D Suite.
plugin/analysis/distance_analysis_diana_2d_3d/start.txt · Last modified: 2019/05/16 07:41 by gilles