OrgaCount - Features

Why OrgaCount?

The web-based application OrgaCount can be employed for almost any kind of counting. Especially for assessing statistics in phytoplankton monitoring procedures, the software offers special algorithms for two major counting strategies: Counting with 'Predefined Size Classes' and 'Ad-hoc Counting' including biovolume analysis.
In addition, two further general analytical modes are available: 'Taxon & Size Class' and 'Taxon Only' mode. They can be well employed for counting other taxonomic groups or events.

In contrast to other applications, OrgaCount runs in a safe server environment connected to the Internet. Alternatively, the application may be installed on a customer's server system or be used locally or for the fied work on a mobile device.

However, web-based installations hosted by AquaEcology have several benefits with regard to the notions of compatibility and accessibility, as indicated below.

Currently, OrgaCount may be used for counting organisms as well as all other types of items (for instance, cell types; events; behavioral stages). In the case of organisms, the programme can be used for counting any taxon generally, but it also has special functions for inferring statistics on phyto- and zooplankton, and macrozoobenthos in particular.

Server version of OrgaCount

OrgaCount can be installed locally on a pre-configured mobile device or on a local server system. Mainly, the application is hosted on AquaEcology secure server systems, which can be accessed from all over the world.

All kinds of installations are easy-to-use systems; you will just need a simple web browser to access your counting application. A server installation generally has got the advantage that it will be possible to have more than one user working on the same database. This is important especially for working groups of bigger institutions and research facilities, being responsible for monitoring activities as well as for carrying out extensive project work.

In addition to that, a server installation hosted by AquaEcology has got even more advantages, such as:
  • Secure access for as many users as you like, at the same time and from all places connected to the Internet
  • 24-hours-availability of the application and the database
  • Automatic backup of your installation and your data twice a day
  • Continuous and automatic update of your OrgaCount version
  • On-line connection to various regional taxon lists that can be downloaded and implemented in the system
  • Access to the most recent plugins being available for OrgaCount

Taking into account these features, comprehensive networking activities can be set up: Different scientific groups working in the same region or monitoring a certain ecosystem will be able to harmonise their efforts by using the same database and standardised taxon lists. With OrgaCount, it will then be possible for all groups to disseminate the information and to compile reports according to pre-defined standards. The system enables the users not only to make use of existing data, but also to feed the database with new and modified information on taxa or images that can be immediately shared among all participants of a project.

Overview of OrgaCount

OrgaCount is following the philosophy of the web-based software system biodivDP (biodiversity data provider), which is also the basis for biological assessment and database applications. Thus, the system is strictly modular and operates within a multi-windows environment enabling the user to work in more than one application at a time:

The OrgaCount environment is well organised in various modules related to each other in a tree-like structure. This allows you to easily understand the relationship between items, and provides an easy navigation flow to the various functions available at each level of organisation. Information is stored by three main levels of organization, from general to specific: projects, samples, and sessions. All tree modules can be expanded and collapsed as needed:

  • Projects hold general information on a working programme that can be defined by a certain institution, a specific geographic location, a grant, etc. One project may contain one or more samples and sessions.

  • Samples are treated in the same sense as they are used in biology and, particularly, in oceanography. They hold information about all data that associated to a real sample, such as codes, information about the collecting site and the local conditions, counting procedures etc. One sample may contain one or more sessions.

  • Sessions only contain those kinds of information related to organism counting processes, such as the microscope settings, the area counted, etc.

Projects, samples and sessions work in very similar ways, and by this creating an easy workflow once you are familiar with the principles of working with OrgaCount.


Within the Projects branch, you have several possiblities of getting and modifying project-related information:
  • Search projects
  • Add new project
  • Show project details
  • Modify project details
  • Delete project
  • Show results for a project
  • Show counting domain settings
  • Add an unlimited number of optional fields


As with projects, the Samples branch provides you with various options:
  • Search samples
  • Add new sample
  • Show sample details
  • Modify sample details
  • Delete sample
  • Show results for a sample
  • Move the sample to another project
  • Show results for a sample or a subset of samples

When choosing 'Add new sample' or 'Modify sample details', a data entry form will pop up, where detailed information on the sample can be entered:
  • Sample code
  • Ship, cruise and station name
  • Geographical information in 3 formats
  • Station and sample depth
  • Date and time
  • An unlimited number of optional fields


At the Sessions level, counting-related details can be entered. This includes information on the used miscroscope, on the counting procedure, as well as the counting layout, which is stored separately for every session. The options are as follows:
  • Add new session
  • Show session details
  • Modify session details
  • Delete session
  • Enter optional fields
  • Show results for a session or a subset of sessions

By opening the 'Counter' branch, the respective counting layout used for that session will be displayed. More detailed information on the counting layout will be given below.


OrgaCount is a complex and comprehensive application. It offers a wide range of functions and possibilities for the user. The user guide as well as the online help functions will assist you in accessing the features of the programme. In order to make the user familiar with OrgaCount in the most efficient way, AquaEcology also provides you with training courses for single participants as well as for groups.

We offer various individual training models:

  • In-house training of single users: One of our training experts will visit your institute/ company/ department and give individual guidance and support to the user.

  • In-house group training: One of our training experts will visit your institute/ company/ department and provide your team with a systematic and detailed overview over the OrgaCount system. Of course, we will regard individual questions and problems.

  • Single or group training in seminar rooms at AquaEcology in Oldenburg. If you arrive from a far location, we will be delighted to assist you in getting a suitable accommodation.

In case you are interested in our training programmes, please, write a short e-mail to

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