Getting started

This manual provides step-by-step guides to briefly introduce the main work steps.

New File - image preprocessing

  1. Menu: File->New data file or click on "new"-icon open in the tool bar
  2. Fill out the form (see figure below)
    • Choose directory and directory structure: Flat Directory or DircetoryPerTreatment
    • Setup image directory
    • Setup data file (output file)
    • Click the check boxes to show Outlines and Gallery BBoxes
    • Clikt the Button Segmentation Setup to adjust segmentation parameters.


Open File

There are three ways to open a data file:

A progress bar and a Abort-button will appear at the bottom of the main window.

Select items in the gallery viewer:

The gallery view has a context Menu. Note the sub menu Quick Sort, which is a efficient and fast way for sorting the gallery.

Sorting and Ranking

After sorting the select item is placed in the upper left corner of the gallery.

Classifier training

Training of a support vector classifier.

Data Export

The Menu Data Export offers three options:
  1. Screenshot of the gallery
  2. Table of class counts
  3. Data table (one line per cell)


Simple box- and bar graphs can be displayed using either the corresponding menu or shortcuts (P+ 1-5). The plots give a quick overview over the class counts and dedicated features.

Following plots are available:
  1. Bargraph grouped by class.
  2. Bargraph grouped by treatment.
  3. Boxplot - Intesity
  4. Boxplot - Size
  5. Boxplot - Standard Deviation of Intesity

Mean intesity per experimental condition grouped by class.