Annotations

Annotations are the main tools for analysis in Pathadin. Drawing annotations, You define the region of interest (ROI)

There are four main types of annotations

  • Line
  • Circle
  • Rectangle
  • Free figure (Polygon annotation)

The annotations (coordinates) can be easily exported pressing the tab “View”, and “Export Annotations”. The generated JSON file can then be shared with everyone using the same slide.

The list of created annotations is available in the lower right window.

List of annotations

Annotations are multifunctional tools. When You expand the annotation by pressing its name, the list of properties appears. Some of them will be used routinely, the others- only in extraordinary cases.

The main properties include:
  • Label: defines the name of the annotations. Double click on the name of the annotation to change it.
  • Figure and Text_graphic_view_config: by pressing “background-color” You can select the color (HEX panes) of the annotation.
  • Stats: displays the basic (length, area) features of the annotation if used with digital slides.
  • Filter_id: for applying the filter inside the annotations.
  • Filter_level: defines the level of magnification, where the filter will be applied.
    • Digital slides are high-resolution pictures with multiple magnification levels. If Filter_level is set to 0, the analysis will be done on the highest magnification equal to the one the slide was scanned at (usually, 20x or 40x).
    • Such high resolution is usually unnecessary and difficult to analyze. Usually, the filter level set 1 or 2, sometimes 3 is enough to make the analysis done- the bigger number, the lower resolution is.

The annotations can be synchronized in multiple windows by pressing the “Synchronize” button.

Synchronization of slides

This tool is applicable in a series of sections, if, for example, there is a need for the simultaneous analysis of the same region on H&E and immunohistochemically stained glasses.