Kurt De Vos
University of Sheffield, Academic Neurology
kurt.devos at iop.kcl.ac.uk
Included in cell_counter.jar, and is released under the GNU General Public License.
Download cell_counter.jar to the plugins folder,
or subfolder, restart ImageJ, and there will be a new “Cell Counter” command in the Plugins menu or submenu.
May not work correctly after using Load Markers to load more than 8 counter types from an XML file.
Opens off-screen on 1024 pixel wide and smaller monitors.
This plugin will open a new cell counter GUI.
On the left are the counter types and counters, on the right the action buttons.
Initialize: Initializes the current image or stack for counting, this will create a duplicate image/stack titled “counter window” – when keep original is checked, the source image remains open
Add: adds a counter type.
Remove: removes the last counter type.
Delete mode: toggles between insert and delete mode. When checked, the marker of the currently selected type closest to the mouse cursor will be deleted when you click.
Delete: delete the last placed marker.
Reset: reset all counters to 0.
Results: Shows the counter results in the ImageJ results table. In case of a stack the counts per slice and the totals are displayed.
Save Markers: Exports the marker data to an XML file – Only available when running java 1.4 or higher
Load Markers: Loads stored marker data from an XML file – – Only available when running java 1.4 or higher
Export Image: Makes a copy of the counter image with the markers written on it (only the current slice is copied in case of a stack)
Measure…: Measures the pixel value at each marker and displays a result window showing: Type – Slice – X coordinate – Y coordinate – Pixel Value
Open the Cell Counter plugin and the image/stack you want to count (if the Cell Counter plugin is already open you don’t need to open a new instance). Click initialize, now you are ready to count features.
Note that at any time you can add types or remove them.
Select the type you want to count, and count by clicking on the feature in the image. A colored number corresponding to the type you are counting will be displayed on the image every time you click, and the corresponding counter is updated.
Add the following macros to ImageJ/macros/StartupMacros.txt, restart ImageJ, and you will be able to change the counter type by pressing “1”, “2”, “3”, etc.
2001/10/17: first version 2002/02/01: bug fixes 2004/06/26: upgraded to work with ImageJ 1.32 2005/12/27: version 2 2006/02/02: No longer requires Java 5.0 2006/02/14: Added “Save Markers” and “Load Markers” buttons 2006/03/06: Added “Export Image” and “Measure” buttons 2006/03/12: Add “Show Numbers” checkbox 2008/02/29: Updated to work with Grid plugin 2008/08/27: Added “Show All” checkbox; works with hyperstacks and composite color images 2008/09/02: Added setType() method to support macros 2008/09/22: Out of focus markers displayed as outlines 2009/07/01: Fixed “Load Markers” bug 2010/12/07: Uses less memory
Authors: Jeffrey Kuhn (firstname.lastname@example.org) The University of Texas at Austin Anthony Padua (email@example.com) Duke University Medical Center, Department of Radiology History: 2000/08/22: First version 2002/10/31:
Author: Wayne Rasband (firstname.lastname@example.org) Date: 2000/8/28 Requirements: ImageJ 1.18s or later Source: SpecifyLine_.java Installation: Download SpecifyLine_.class to the plugins folder and restart ImageJ. Use the
Author: Wayne Rasband (email@example.com) Date: 2000/8/17 Source: Circularity_.java Installation: Circularity calculations are built into ImageJ 1.29 and later. Check “Circularity” in Analyze/Set Measurements and the
Author: Wayne Rasband (firstname.lastname@example.org) History: 2000/11/28: First version 2003/01/28: Uses the image or selection min and max; works correctly with signed images Source: SixteenBit_Histogram.java Installation:
Author: Markus Hasselblatt (MHasselblatt@zyomyx.com) Date: 1999/11/16 Requirements: ImageJ 1.10 or later Limitations: Only works with 8-bit images Source: Auto_Corr.java Installation: Copy Auto_Corr.class to the plugins
Author: A. Karperien, Charles Sturt University, Australia History: 2002/08/26: First version Requires: Java 2 Source: enclose_.java Installation: Download enclose_.class to the plugins folder and restart