Colony Counter

Author: Bruno Vieira
University of Lisbon, Faculty of Sciences
mail at bmpvieira dot com
Source: Included in Colony_Counter.jar, and is released under the GNU General Public License.
Limitations: Requires Java 1.6
Installation: Download Colony_Counter.jar to the plugins folder, or subfolder, restart ImageJ, and there will be a new "Colony Counter" command in the Plugins menu or submenu.
Description: This plugin was created to count bacteria colonies from agar plates images. The obtained values are displayed in a "Results" table and can be saved in *.xls file format. When the image is closed, a file named * is automatically saved in the current folder, so that the next time the same image is opened, the plugin won't have to recount that image and can simply load the results from the * The plugin's interface is simple, on the left are the functions buttons, on the right the input fields for the settings. Except for the "Delete mode" and the "About" buttons, all the others have a keyboard shortcut (visible inside square brackets on the button's name) that can be used when the mouse cursor is placed on the image.


  • Open image: Opens an image and automatically counts it's colonies, or simply loads and display the saved * from a previous count. The number of colonies is added in a new row to the "Results" table.
  • Open next: Replaces the current image with the next one in the same folder and do the same as "Open image".
  • Count folder: Counts and/or loads the * for all images in the current folder, and replaces the current "Results" table with the new results.
  • Add colony: Adds the currently selected area as a colony allowing correcting the automatic count. The last value in the "Results" table and the * file are updated.
  • Delete colony: Activates/Deactivates the "Show all" function of the ROI Manager, allowing selection of a colony by clicking on it's number on the image, and then deleting it by pressing the keyboard letter "d".
  • About: Shows the "About Colony Counter" message window.
  • Size fields: Allows setting the minimum and maximum limits for the size of colonies that the user wants to detect and count. Pressing the keyboard key "Enter" in any of these input fields will delete the previously saved * and recount the image with the new settings, saving a new * when the image is closed or replaced by "Open next".
  • Circularity fields: Does the same as above but for circularity.
History: 2009/10/20: first version (0.9)

|Plugins | Home |