Getting started

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

• New File (image preprocessing)
• Open file (preprocessed data)
• Segmentation
• Select items in the gallery
• Sorting and ranking
• Classifier training
• Data export
• Plots
• List of Applicaton Shortcuts

New File - image preprocessing

1. Menu: File->New data file or click on "new"-icon 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.

Segmenation

• Select a color channel for primary segmentation (drop down menu in the upper left corner).
• Select a segmentation algorithm (drop down menu in the uppler right corner).

Open File

There are three ways to open a data file:

• Menu: File->Open File
• Press the Open File icon in the tool bar
• Drag & Drop: drag the data file from the file manager and drop it in the main window (anywhere, except in the central gallery viewer)

Select items in the gallery viewer:

• Douple click on an item. (selects only one item)
• Click on multiple items while the Ctrl-button is pressed
• Drage the mouse over multiple items while the Ctrl-button is pressed

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

• Refresh - updates the display (shortcut "F5").
• Select all - select all items in the gallery.
• Invert selection - invert selection in the gallery.
• Quick Sort - sort the items by cosine similarly, the currently selected item(s) serve as reference example for the similarity measure.

Sorting and Ranking

• Select at least one item in the gallery.
• Click on the Quick Sort button in the toolbar or
• Click on the Quick Sort button in the context menu

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

Classifier training

• Choose a classifier in the drop down menau (SVC, One class SVM or Manual Classifier)
• Setup the classes ( button in the tool bar)
• Select items in the gallery and press the -button to assign the sample to a certain class.
• Hover the other buttons and controls to see tooltips
• There is a big button labeled "Predict"

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)

Plots:

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