Sync Windows and Sync Measure 3D

Author: Joachim Walter (walter at
Source:Contained in Sync_Win.jar, which can be opened using a ZIP utility
Installation: Download Sync_Win.jar to the plugins folder, or subfolder, restart ImageJ, and there will be two new commands (Sync Windows and Sync Measure 3D) in the Analyze/Tools submenu.

Note that Sync Windows is built into ImageJ 1.46f and later as the Analyze>Tools>Synchronize Windows command.


Sync Windows

The Sync Windows plugin synchronizes mouse motion and input between multiple windows. Thus, an ROI drawn in one window is replicated in all other synchronized windows in the synchronized window set. A synchronization cursor (the red box above) indicates the location of the mouse in all synchronized windows.

It is an enhanced version of the SyncWindows_ plugin by Partrick Kelly (part of the UCSD package) that adds the following new features:

  • Optionally passes on changes of the z-slice in a StackWindow to other synchronized StackWindows.
  • Optionally translates positions to different windows via offscreen coordinates, providing correct registration at different zoom levels.
  • Has an "Update Window List" Button, so that it is not necessary to restart the plugin for adding a newly opened window.
  • Is not disturbed by closing windows while the plugin is running.
  • Can handle Polyline selections.
Sync Measure 3D
Synchronizes the cursor and z-slice in all selected windows, 
and performs measurements on 3D ROIs in all selected windows.

- Load the data, each color channel as a separate 8- or 16-bit grayscale stack.

- Run Sync_Measure_3D. (Analyze>Tools>Sync Measure 3D)

- Synchronize the windows, in which you want to measure by selecting them in the
    window list.

- Click "Start Measurements".

- Click on "Projection" to obtain a combined maximum intensity projection of all
  selected images (stacks). This projection is not used for measurements, but is
  synchronized with the other images and might be a convenient reference.

- Choose a threshold for each image.

- Measure gravity center, Volume, Intensity and distance to preceding stacks:
    o Draw a ROI around the particle you want to measure. If the particles in different
        channels are at different positions, turn "Synchronize Cursor" off for that.
    o If necessary (when other particles are inside the ROI in different z-slices),
        Select first and last slice to include this particle and exclude the other ones.
  o Double-click (left mousebutton) into the ROI to perform a measurement.
        + The X, Y and Z values are the coordinates of the intensity gravity centers
            of the measured objects.
        + The Volume and Intensity values are the volumes and the total intensities
            of the measured objects.
        + The Dist 1, Dist 2, ... values (for 2 or more image stacks) are the 3D distances
            of the intensity gravity center of the object in the current stack to the intensity
            gravity center of the object in the first, second, ... stack in the list.
        + If the scale of the image is not set, the results are displayed in "pixels".
            3D-distances are meaningless in this case, if the distance between slices
            differs from the pixelsize. If the image scale is set, the results are displayed
            in the selected unit.
        + Intensity values are given in gray values or the selected units in case that the
            image has been density calibrated. If the image is density calibrated, the centers
            of mass are calculated with the calibrated values, but the threshold is still a raw
            value (0-255 for 8-bit images).
    o To calculate mean values and standard deviations, click on "Stop Measurements".
        + For the x- y- and z- coordinates the differences to the coordinates of image stack #1
             are calculated ( (value for this stack) minus (value for stack #1) ) and their mean
             and standard deviation values are displayed. This helps in calculating the chromatic
             shift to stack #1.
        + For the Dist 1, Dist 2, ... values, simply the mean and the standard deviation are
See Also: Image5D
Spectral Unmixing Plugins
History: 2002/03/11: First version
2002/04/01: Fixes zooming bug
2002/06/19: Added Sync_Measure_3D plugin
2002/10/07: Slice spacing used when calculating volumes
2004/02/22: Updated
  • When Sync_Windows is active, the ImageJ Statusbar shows the intensity value of the image, which contains the "main" cursor (corrects a previous bug).
  • New crosshairs Sync cursor
  • Sync_Windows is displayed in the window list.
  • Sync_Measure_3D now measures on "Space-click". (Alt-Click and Shift-click no longer work as they are used to add parts to and remove parts from ROIs)
  • Sync_Measure_3D works on 16-bit images.
  • Threshold values can be typed into text fields in addition to setting them with the sliders.
  • z-Positions measured by Sync_Measure_3D are now consistent with the cursor position displayed in the ImageJ window.
  • The size adapts better to smaller screens.
2004/10/24: Now measures on double-click. Space-click in v1.2 was a bad idea, because if a button in the control window still has the focus, it gets "pressed" by pressing the spacebar. Also, pressing the spacebar while scrolling through 16-bit image stacks resets the Min- and Max-values.

2005/06/03: Updated to work with Image5D

2005/07/09: Works with AND WITHOUT Image5D

2006/04/19: Version 1.5

  • Uses the new ImageListener interface to update the image list. This also works with Image5Ds when version 1.1.5 or higher of Image5D is installed. Needs ij 1.37b or higher.
  • Can use the image scaling and offset values for determining cursor positions in synchronized images. This only works correctly, when the images have the same length unit i.e. the difference between 10nm and 10um is not recognized, but the difference between 10um and 0.01um is.
  • Frames and Channels of Image5Ds can be synchronized.
  • Corrected a compilation problem that would make Sync_Measure_3D unresponsive at the first measurement when measurements were performed in spatially calibrated images.

2006/10/02: Version 1.6

  • Works with Image5D v1.1.6, which sorts base Image5D classes in a package structure.
  • Fixed a bug: Cropped images from synchronized windows are not equally sized when the ROI is selected at zoom <100%
  • Fixed a bug: For the active window of several synchronized images the position values are not updated in the statusbar.

2007/08/14: Version 1.7

  • Works with Image5D v1.2.0 (where Scrollbars for z and t have been changed).
  • Also synchronizes slices (channels, frames), when they are changed by moving the mousewheel.
  • Sync Windows is built into ImageJ 1.46f and later as the Analyze>Tools>Synchronize Windows command.

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