Cell counting tool


Cell counting tool (CCT) is developed by Environmental Microbiology Technology Group in Research Center for Eco-Environmental Sciences, Chinese Academy of Science.

The CCT is a windows-based software tool developed to record and process algal cell count data while it is being generated manually by a microscope technician.

Counting options include the user’s preferences of full field of view, transects, at the chosen magnification. The user is able to easily construct a list of types seen in the sample from a stored list which includes links to web-based photomicroscopy images to aid with identification.

In addition, the user can choose to count and record data for a range of units including single cells, filaments (trichomes) or the area for colonial types such as Microcystis. This accommodates the complexity of how to count and quantify colonial species and genera of cyanobacteria in particular.

The software library already includes the approximate geometric shapes for all types of cells which can then be used to automatically calculate and record biovolume for each species counted.

It is also possible to record and hyperlink photos taken of species and cell types from the user’s individual sample being counted for later checking and also for including in reporting.

The software includes the ability to record the map coordinates of the sample site and later to include a map of the sites in a report. The geolocation information is established in the database for each new site (need to include the source of data used for mapping and constructing image maps).


The following windows components are require to run the CCT:

  • Windows Installer 4.5
  • Microsoft .NET Framework 4 (x86 and x64)

If the above components are ready, you can click and install the application here.

Otherwise, please click here to install the components first, and then install the application here.

If the software are not able to run, it is possible to completely remove by download uninstall.zip, and subsequently unzip it, open uninstall.bat to remove CCT.

How to use

The usage of this CCT can follow the following videos (Unfortunately, in Chinese, passwords are required for play the videos, which is rcees2018emt);

Ming Su
Ming Su
Associate Professor of Environmental Engneering

My research interest is water quality problems in drinking water bodies, with a focus on harmful algal blooms and associated taste & odor problems.