Object Analyzer for version 3.5 and higher
The interactive object analyzer tool for 3D microscopy images in Huygens Essential and Huygens Professional allows you to obtain statistics of individual objects by clicking on them, or analyzing all objects with a single button press.
The image is segmented into objects by an effective seed-threshold level, and connection technique. A third method that can be applied is the watershed method which increases the reliability of the segmentation further. To remove too small objects in an early stage from the analysis a garbage level can be set below which objects are discarded. After that, detected objects are automatically labeled and sent to a continuous Iso Surface Ray Tracing renderer.
Predefined filters allow to remove objects with different properties before further analysis.
The segmented and labeled image is shown as a colored iso-surface image. Each object is assigned a different color. Because the iso-surface renderer can recompute a new iso surface rapidly, the threshold can be manipulated interactively.
By clicking on an object the user can read off the local statistics.
The following statistics are reported for each object, depending on the selected Experimental Preset:
- Geometrical data
- Spatial location
- Relation with neighbors
- Relation with reference objects
- Degree of overlap (colocalization)
Multiple render pipes
The iso surface renderer is equipped with two surface 'pipes'. Each pipe is able to segment, label and render a channel of the image independently. When two overlapping objects are clicked on the statistics of both are reported.
A third pipe is reserved to show a MIP projection of a channel, to serve as spatial reference.
See real size image: <kbd><a href="display44">reference_frame_total_OA_3.6.0.png</a> <small>(210.7 kB 2010-06-03 12:09:06)</small></kbd>
Data: cell nucleus FISH-stained recorded at the Nuclear Organization Group
, SILS, University of Amsterdam (head: Prof. Roel van Driel), under the 3D-Genome Research Project.The analysis can be confined to a limited region by selecting a 2D region on the screen.
More features
- Segmentation based on the image histogram
- Interactive definition of 3D Regions Of Interest (ROI)
- Measure object location inside the ROI
- Configurable parameter list, that can be stored in user presets.
- Save the analysis history as a template for repetitive tasks
- Advanced object filter based on any of the reported parameters
- Extensible capabilities by using analysis applets
The ROI tool as a versatile cropper
Because the ROI can act directly on the image data the Object Analyzer can also be used as a independent preprocessing tool for visualization or for example colocalization analysis.
How to use it
For step-by-step introductory tutorials, please see
- Object Analyzer Tutorial .
- Object Analyzer Expert Tutorial .
- Module components reference: Object Analyzer Reference.
If you are looking for the tutorial of older versions of the O.A., please see
- Object Analyzer Tutorial 3.4 .
- Object Analyzer Expert Tutorial_3.4 .
- Object Analyzer Reference_3.4 .
Even older (3.2 and before):