NEW Spots

The spots component has been completely revised. The NEW spots collect all the features of the old “spots”, “spot”, and “track” components. The spots creation process as well incorporates all these features. This allows to set up self-contained segmentation parameters. In order to set up parameters for segmenting large images, a region of interest can be defined during creation, and as final step, the entire image is being processed. Furthermore the visualisation for spots and tracks has been improved to display a huge number of objects.

Spots Creation Wizard

• With Back you return to the previous window of the create wizard.
• Press Next to proceed with the next window of the create wizard.
• Click on Finish to calculate the desired spots and display the spots in the viewing area.
• If you do not want to create spots and/or tracks click on Cancel.

Overview

This is the flow diagram of the spots create wizard. For further details please refer to chapter:

Start   Algorithm   Region of Interest     Source Channel Classify Spots     Spot Region Type Spot Regions       Edit Spots   Tracking Classify Tracks     Complete ROI     Finish

Algorithm

• Specifies the path through the creation wizard.
• Process region of interest?
• Process entire image at the end?
• Activate this options, if only a part of the image is interesting, or if the image is to large in order to find good parameters (because calculation takes to long).
• Compute spots with different diameter (region growing)?
• Perform tracking?

• Specify one or multiple regions of interest. If the entire image is being processed at the end, it is recommended to
  specify regions, which contain signals of background and object.

• Create Spots and Tracks only within one or more regions of interest.
• Interactive setup for position and size (default ROI size is limited to 100 MB).
• Allows to find efficiently segmentation parameters for a huge image (using only a subset of the entire image data).
• Allows to segment different regions with different parameters.

• Select source channel and enter an estimated diameter.

• Specify a filter sequence to separate good and bad spots.
• Choose as many filters as you like. Each statistics value type can be used as filter (see menu “edit / preferences / statistics / spots”).

• Segment image from absolute threshold (like iso surface), or from local contrast.

• Specify how the diameter of a spot is computed.
• Automatic or interactive segmentation for spot regions.
• Orthogonal slicer or volume rendering as preview.

• Manually adjust spots before the tracking.
• The dialogue is not available, if the entire image should be processed at the end. Manually edited spots would be lost.

• Specify tracking algorithm type and parameters.
• Brownian motion / autoregressive motion / connected components.

• Specify a filter sequence to separate good and bad tracks.
• Choose as many filters as you like. Each statistics value type can be used as filter (see menu “edit / preferences / statistics / spots”).

• Performs all the calculations for the entire image (for a huge image this maybe takes a while).

• Settings for Spots AND Tracks.
• NEW: Spots visualisation as center points

• Replaces earlier “sorting” tab.
• Filtered Spots or Tracks are highlighted as selection.
• Automatic filter threshold based on statistical distribution (two means threshold).
• Selection can be copied as new Spots component within the Surpass scene.
  

• Statistics contains ALL the values (earlier versions of Imaris
  were only able to display some aggregated values).
• Export as file (can be read by Excel and OpenOffice Calc).
• Interactive two-way-selection. Select in 3d => corresponding
  row in statistics table is highlighted. Select in statistics table =>
  according object in 3d is highlighted.
• Selection can be copied as new Spots component within the Surpass scene.
  

We noticed that the spot detection works much better, if the diameter is underestimated. This fact leads either to a good spot detection with bad voxel statistics, or to a bad spot detection with (good) voxel statistics. For this reason, we decided to adjust the algorithm for the new spots in Imaris 6.0 a little bit. In order to get the same spot detection with the old and the new version, you have to scale up the old estimated diameter by 4/3.  

Example:  

Imaris 5.7 estimated spot diameter 3 um
Imaris 6.0 estimated spot diameter 4 um

The drift correction is available with new features. On the tab "Edit" you find the button "Correct Drift" with the new parameters:

• Embed/crop dataset.
• Correct track positions.

Gamma = 1 Gamma = 2

• Interactive adjustment of gamma for display.
• More colorful volume rendering in blend mode.
• Makes dark regions brighter without changing original image intensities.
• Click onto middle triangle in the display adjustment dialogue and drag it to the left to increase brightness.
  

• Andor: Multi-Tiff (series)
• Biovision: IPLab (MAC)
• MRC
  

• LIF64
• Compressed Axiovision

• Updated Reference Manual for new Spots (Manual as pdf on Download Page)
• Updated Quick Sstart Tutorials for new Spots (Tutorial as pdf on Download Page)

Segment index is now exported to Excel statistics.

• Select the “Edit” tab, and press “From index...”.
• Enter the index number of a specific segment. The corresponding segment is highlighted in 3d. The index of a selected segment can also be inspected on the “Settings” tab.

Any feedback on the installation, and the usage of Imaris and its features are welcome. Please send your comments to support@bitplane.com