The STEPanizer © stereology tool

is available in its first final version.

STEPanizer is a straightforward Java-Program for manual stereological assessement of digital images

Published in the Journal of Microscopy, 2011: PubMed

STEPanizer is a tool for processing images that are already generated according to an appropriate stereological sampling.

It is crucial to accomplish a consistent stereologic sampling including material extraction, tissue handling, tissue sectioning and image acquisition!


STEPanizer is written in JAVA an requires a PC, MAC or LINUX system with installed JAVA JRE [Java Runtime Environement], installable from and a keyboard featuring a numerical keypad (see Manual)

Recent Information! (April 2015)

OFFLINE deployment mode of STEPanizer / MAC issues.

Since June 2014 STEPanizer is only working as offline version. For security issues of JAVA Applets online execution was blocked by the JAVA community.

It is recommended to still upgrade to latest JAVA version to prevent security problems: (current version [April 2015] Java 1.8.0_40)

Current STEPanizer compilation: Stepanizer1-8.jar. It is recommended to use this version.

Some older MACs do not support upgrades to higher JAVA versions. For that issue older compilations are available in the ZIP file below (JRE 1.6 and 1.7).

Since MAC OS X 10.10.x (Yosemite) JAVA is no longer installed by default. Install it on your own from .
In addition, security policies since OS X 10.10.x block JAVA applets from non-registered developers. To circumvent follow the instructions below.


STEPanizer's so-called web-based (ONLINE) JAVA-Applet mode (as published), is now abandoned.

No warranty is given for any damage or loss of data.


updated: April 1st 2015


    Offline Deployment:

    • Download ""
      containing STEPanizer version 1 [subver 0.22 offline] compilation 1-8 (including versions 1-6 and 1-7 for compatibility issues)
    • Save ZIP file on local disk
    • Unzip the folder "Stepanizer1" inside the ZIP to your local disk, e.g. "/Desktop/Stepanizer1/"
    • PC: Double-click on "Stepanizer1-8.jar" in the "/Stepanizer1/" folder
    • MAC: you must have admin privileges.
      Press <ctrl> key while clicking once on the JAR file, choose "Open" and reconfirm "Open" in the 2nd pop-up.

    • ReadMe files for information about compatibility issues on MAC/PC available in the ZIP.

    Further Development (beta versions)

    • Download ""
      (containing STEPanizer BETA 2 (subversion 0.28 offline) as of
      June. 27th 2014, How to install: see above, version 1)

      • Disector enabled, new with SPACE bar toggling
        (you require well aligned and positioned disector image pairs!)
      • Grid 1:2 and 1:3 subsampling (line length not calculated!)
      • Circle grids for 2D boundary assessment (experimental)
      • Measure lengths in SCALE mode (not during COUNTING)
      • New WIDE screen option for notebooks (900x1400 pixel)
      • ROTATE image button for making visible the scale bar during SCALE

      This is BETA Version and the further development of version 1.
      It contains some experimental approaches which are nor further commented or supported.
      During BETA phase saving of parameters can not be guaranteed. Change of version may result in impaired restoration of former settings. Export assessed data with the "Export" function. Write down parameters (testsystem type and number, frame width, display size etc.)
      Try out this version, play arround and send comments, suggestions and critics to me (

Folder for WP Excercise
Excercise images 4 series with one zip file each. Copy to your computer, unzip the folder "SerieX_nn-n" to known location.
Exercise folder for stereology workshop 2016 copy to your computer, unzip the folder "STEPanizerExercise" to known location.

other Java Applets
by S.A. Tschanz
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by stschanz, 2015