Imaris | Release Notes and Bug Fixes

Imaris 6.0.0 Release Notes

Welcome to the Imaris 6.0.0 release notes. Version Date: Nov 27, 2007. 
Please have a look to the Overview of Imaris Release notes for information about prior released features and fixed bugs.

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Imaris

NEW Spots

NewSpotsIcon

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

WizardButtons

  • 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?
Region of Interest 
  • 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.
ROI

ImageROI

  • 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.
Source Channel 
  • Select source channel and enter an estimated diameter.
Classify Spots 
  • 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”).
Spot Region Type
  • Segment image from absolute threshold (like iso surface), or from local contrast.
Spot Regions
  • Specify how the diameter of a spot is computed.
  • Automatic or interactive segmentation for spot regions.
  • Orthogonal slicer or volume rendering as preview.
Edit Spots
  • 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.
Tracking
  • Specify tracking algorithm type and parameters.
  • Brownian motion / autoregressive motion / connected components.
Classify Tracks
  • 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”).
Complete ROI
  • Performs all the calculations for the entire image (for a huge image this maybe takes a while).
Spots AND Tracks Settings
SpotsSettings

SpotsSettings

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

SpotsFilter

  • 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.
Spots Statistics
SpotsStatistics

Statistics

  • 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.
Spots Restrictions Restrictions depending on Modules / Products.
The features illustrated above require Imaris, MeasurementPro, and ImarisTrack. Without MeasurementPro, the “Filter” and “Statistics” tab are not available. Without ImarisTrack, the track creation steps, and the track settings are not present.
Spots Compatibility Spot and Track information from old scene files (Imaris 5.7.2 and earlier) will be ignored.
Important Note for Estimated Spot Diameter

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

Drift Correction

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.
Semi-automatic Surface Segmentation Single objects can be added by one easy mouse click. Select “edit” tab of surface object (Iso surface split). There are three different techniques available:
Edit Surfaces

EditSurfaces

Rayburst  
  • Optimized for objects which are similar to a sphere.
  • Position the autodepth cursor to the center of the object
  • Adjust the size of the box to the approximate size of the object (using the mouse wheel).
  • Shift-click to create the new object.
Rayburst
Marching Cubes  
  • Optimized for objects with a complex rough surface
  • Position the autodepth cursor to the center of the object.
  • Adjust the size of the box to the approximate size of the object (using the mouse wheel).
  • Shift-click to create the new object.
MC
Magic Wand  
  • Optimized for single,c complex objects, which are located over a larger region of the image.
  • Position the autodepth cursor to the border of the object (the size of the box does not influence the result).
  • Shift-click to create the new object.
MW

Gamma Adjustment
GA
Gist1
Gamma = 1
Gist2
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.
New File Readers
  • Andor: Multi-Tiff (series)
  • Biovision: IPLab (MAC)
  • MRC 
Updated File Readers
  • LIF64
  • Compressed Axiovision
Updated Manuals
FilamentTracer

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.


Fixed Bugs (since Imaris 5.7.2)
ID Summary
2726 Pressing 'q' in Surpass kills Imaris
2705 volume painter: changing the diameter of the disk by typing a number does not change the box of the 3d cursor
2694 Frame Shading has a memory leak
2680 Resample open displays cropped image the second time
2677 InPress recall of Figure view by double-click doesn't work
2660 resampling open: unable to handle manipulato in y for LIF-image
2657 FpBp: LSM objectfive description is not beeing put into correct field BP_ObjectiveDescription
2627 edit file type associations does not work under windows vista
2562 Split Spots XTension broken if Surpass Scene deleted
2558 DeltaVision datasets bigger 2 GB can not be read
2551 Keyframe Animation is overwritten without warning
2546 FpBp does not find license, if only "Imaris x64" is installed
2541 filament statistics aggregation for segments with the same depth does not work
2534 Zeiss LSM data crashes Imaris or display is corrupt
2482 ZVI files are not read correctly
2480 Display adjustment dialog is not restored, if Imaris is started via COM-Interface
2465 A time animation of surfaces allocates memory until it crashes
2463 Negative Duration, Track Speed...
2459 Zoom factor negative
2435 Only spots of the first Spots object in the surpass tree can be edited
2428 Imaris x64 reports under Vista64 a to large number for free memory blocks
2412 leica sp5 reader does not support large data
2411 File Converter can not be started from Imaris File Menu
2407 Custom tools appear when Matlab is not present
2403 Specific Folder Only For Newly Added Files
2394 Zeiss LSM compressed can not be read
2391 License server does not accept full server name
2390 Explorer crashes when 'information bubble' is displayed
2386 Time calibration lost after 'Swap time and Z' and back
2385 Imaris can not read some LIF-Files stored with Leica SP5
2383 binary multi-slice TIFF file is loaded as corrupted image
2346 Zeiss LSM 2D dataset channel 1 loaded in both channels
2319 Does not negotiate Ports on RLM server correctly
2315 areas of the GUI using right-click need "show help" disabled
2289 Zoom value in Surpass wrong (100%-button does not adjust camera to display one voxel per pixel)
2279 LSM dataset last layers brighter, radom max intensity
2268 The spot quality threshold label is written very very small on Mac
2201 Tiff not recogniced as part of LEI set
2176 Installation shows 'Unknown Publisher' warning
2166 Can't manually place spots in depth via orthoslicer
2106 Region Growing local contrast can not set threshold
1874 Building inventor graph can take a very long time for many spots.
1688 Rebuild does not keep a custom resample size and sigma
1554 The statistics viewer cannot be dragged
612 MetaMorph STK 2D time read as 3D stack

Feedback

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


Last Modification: AS, 27-NOV-2007

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