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DisectCounter

BASICS

Steps

Program estimates the total number of objects in 3D volume from two 2D sections using "Disector" method. The typical succession of steps is:
  1. Align images of 2D sections.
  2. Define region of interest.
  3. Define stereological counting frames.
  4. Label objects terminating between sections.
  5. Estimate total counts.

Download and installation

Program requires Windows 10 operating system.
Install program from Microsoft Store free of charge clicking HERE .

Features

  • Simple, intuitive and user-friendly interaction.
  • Fast graphics based on Win2D technology.
  • Estimates and exports values from 5 counters.

DISECTOR PRINCIPLE

The total number of objects in 3D volume can be estimated by counting the objects terminating between two (properly sampled) 2D sections. Fig.1 shows the situation where only the cell visible on the first section but not in the second one is counted, the cell visible on both sections is not counted. Region of interest outlines the region where the cells are counted. Stereological counting frames are selected areas where the counting is performed and used for the total count estimation. Only framed overlapping with ROI are taking into account. (see e.g. the review paper of Slomianka for details).

Fig. 1. Disector principle. a) 3D volume intersected by 2 planes. b) Cells distinguishable on Reference image but not on the Lookup one are marked green and counted. Cells visible on both images are marked red and not counted.

FUNCTIONS

Program consists of preparation of stereological counting scheme and the counting itself.

PREPARING OF COUNTING SCHEME

  • Images loading
    Click the Load 2 images button to select pair of images. If you only want to test application, you can load built-in demo images by pressing "ALT" + "D" keyboard keys.
    Images are displayed side-by side (Fig. 2.), use CTRL + mouse wheel to adjust zoom if required.
  • Images aligning
    Check checkbox ALIGN, then click 3 well-identifiable positions on the left-side image and corresponding 3 positions on the right-side one in the same order (see Fig.2).
    Press the button Align images which rotates and shifts the lookup image to aligned position (Fig. 3).
    Watch cursor on the left image and the cross-like cursor on the right one. In properly aligned images they both should point to the same structure
  • Region of Interest (ROI) setting.
    ROI covers the whole image by default. Check DRAW ROI to define new ROI by clicking the border polygon points.
    Button Close contour closes the polygon and terminates drawing. Undo button erases the last clicked point (the same effect can be achieved by right mouse click.
  • Stereological counting frames setting
    By default, the counting area is the whole image and Area fraction AF=1.0.
    Check USE FRAMES to define the Size and the Distance of stereological counting frames.
    Use RANDOM button to shift frames randomly. Value AF=... shows the ratio of counting frames area / Roi area.
  • Configuration
    The buttons Save and Load archive Align, Roi and Frame parameters in file. Positions of clicked points obtained in Counting mode are stored and restored too.

Fig. 2. Aligning marks. Three points on corresponding positions should be clicked on both images.

Fig. 3. Aligned images. Algorithm computes scale, rotation and translation values that transform lookup image to aligned position. Left side shows reference image with drawn ROI (blue) and counting frames that overlaps with ROI.

COUNTING

  • Preview
    PREVIEW checkbox shows a lookup window preview "flying" inside the reference image. Such side-by side arrangement of both images allows their quick visual comparison.
    The image Brightnessand the Size of the preview window can be changed by the corresponding controls.
  • Counters
    By default, Counter0 is incremented on mouse click and Counter1 by click + SHIFT key press. Counter1 is selectable and can be replaced by Counter2-Counter4.
    Text boxes on the right side show the counters content and estimated values calculated as value/area fraction.
    Reset all clears all counters while Reset clears only the selected one.
    UNDO removes the last clicked point.
    Results shows a table containing values and estimated values of all counters. This table can be Copied into clipboard and subsequently pasted into external program (e.g. Excel) for further evaluation.
    Function Zoom in magnifies a frame clicked by right mouse to the full screen size. On return Zoom out zooms the reference image to full screen size.

Fig. 4. Preview window inside the cyan rectangle represents the part of lookup image. This window is "flying" above the cursor on reference image. Left part shows counted position (green), the right side represents the not counted one (red).

MOUSE AND KEYBOARD CONTROL

Zoom image CTRL + mouse wheel
Scroll image CTRL + left mouse drag and drop
Increment Counter 0 (in counting mode) left mouse click
Increment selected counter (Counter 0 - Counter 4) SHIFT + left mouse click
Undo last clicked position right mouse click + Undo menu item
Zoom clicked frame to full screen size right mouse click + Zoom in menu item
Zoom clicked reference image to full screen size right mouse click + Zoom out menu item

License agreement

Copyright (C) 2020, Institute of Experimental Physics, Slovak Academy of Sciences, all rights reserved.
This software is provided by the copyright holders and contributors "as is" and any express or implied warranties,including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall the copyright holders and contributors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.