The Leibniz Institute for the Analysis of Biodiversity Change

is a research museum of the Leibniz Association




Quick facts

Project title: 
3D Accounting and Measuring Plugin
ZFMK Project lead: 


A New ImageJ – FIJI Plugin for Counting Objects in Bi-Color Images


Reliable methods for automatically counting objects in images are scarce, when the objects involved lie in close proximity to one another and/or have unclearly defined edges. We created 3D-AMP, a new plugin for the existing FIJIA - ImageJB software package, to reliably analyze image stacks containing these previously hard-to-quantify objects.

Pixel Based Counting vs. Currently Available Methods

Currently available object counters rely on object recognition software, also called blob detection software. They show extreme inaccuracy when the objects they count are in close proximity and/or lack welldefined borders. 3D-AMP uses pixel-based counting, a far more accurate method. This allows for the estimation of the total number of objects if they have a similar size, by measuring a small number of individual objects and then calculating the average number. 3D-AMP was as accurate as manual counting in 2 independent tests: p = 0.44 and p = 0.29.


  • Easy to use, prompted graphic user interface and instruction guide.
  • User-defined region of interest (ROI) – allows the separation of areas within each channel. 3D-AMP will count the pixels inside and outside the ROI.
  • Alignment tool – stabilizes image stacks against sample or microscope movement during image capture.
  • Threshold tool – only allows pixel counting above user defined threshold, used to reduce noise and background fluorescence/staining.
  • Pixel to unit converter – data is automatically converted from pixels to the user’s unit of choice and both values are exported.

This plugin works with

You can use most kinds of (hyper)stacks with one or more channels in the common
image formats.

Conditions of use:

You are free to use this software for research purposes, but you undertake to include a citation or acknowledgment whenever you present or publish results that are based on it. ZFMK makes no warranties of any kind on this software and shall in no event be liable for damages of any kind in connection with the use and exploitation of this technology.


Contact person

+49 228 9122-247
+49 228 9122-212
peter.ruehr [at]


Version 1.2.0