Imaris | Release Notes and Bug Fixes

Imaris 6.1.0 Release Notes

Welcome to the Imaris 6.1.0 release notes. Version Date: Apr 29, 2008. 
Please have a look to the Overview of Imaris Release notes for information about prior released features and fixed bugs.

[Imaris
[MeasurementPro
[FilamentTracer
[ImarisColoc
[ImarisXT
[Fixed Bugs
[Feedback]
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Important Note (Windows only):

Before Installing 6.1.0 please uninstall ALL older versions of Imaris (6.0.1 and older)! 
There is a bug in older Imaris Versions which will be "activated" by installing 6.1.0. The bug causes a significant longer startup time, and ImarisXT will not work any more. There is a patch version 6.0.2 available, which doesn't have this issue. Imaris 6.1.0 and 6.0.2 can be installed togehter. Imaris 6.0.2 is available from the Software Release Archive


Imaris
 NEW Surfaces The easy to use Creation Wizard is now available also for Surfaces, and Surfaces Tracks. The Wizard has been newly designed and contains new labels for each category for easy recognition. This userfriendly data processing subsystem in Imaris will accompany your work in Imaris for most processes from now on. Benefit: Fewer components in the object tree and more autonomous components, which store data and reproduction information. High recognition value.

 Creation Wizard
Imaris 6.1 introduces a completely new Surfaces Object. Replacing the old IsoSurface Object, the new way to generate surfaces is userfriendly and timesaving. To signify this change we have not only changed the look of the Creation Wizard, but also changed the Surfaces Icon. Please find the according chapter in the Imaris Reference Manual for more details.
Algorithm
In the first window of the Creation Wizard you find the algorithm settings. Here you have to decide, if you want to segment only a Region of Interest (ROI), if you want to use the Seeded Region Growing for the Surfaces detection, and if you want to create Tracks after the Surfaces detection.
Region of Interest
With the new subregions you can keep Imaris interactive even when working on very large images. The Creation Wizard saves all parameters and processing instructions so that the computation can be repeated for the same region, a different region, or the entire image. This enables fast parameter tuning: try on regions, apply on full image later, or re-apply previously defined image processing sequences on different region or image.
Source Channel
Here you'll select the image channel, which will be used for surface detection. You can also set up the smoothness of the resultin surface area, and if needed remove artefacts from non-uniform background intensities.
Threshold
Threshold can easily be set interactively with preview. In earlier Imaris versions you would need to finish the IsoSurface calculation first, and then rebuild it, if the threshold was not optimal. Now you can immediately see the result, while adjusting the threshold.
Classify Surfaces
The resulting surfaces can now be classified / filtered (also with interactive preview). Small Surfaces may be removed using the "Volume" filter. In addition you can use many other filter types like "voxel Intensity", or "Sphericity", etc.
Tracking
If you loaded a time series, the objects can now be tracked. The available algorithms are the same as for the Spots Tracking (please note: in order to use Tracking, you need the "Imaris MeasurementPro" and the "ImarisTracking" module).

Properties
 Settings has options for visualisation (surfaces, center points, tracks).
 Creation shows the creation parameters, and allows to rebuild the surfaces.
 Edit lets you add or remove surfaces, cut surfaces into pieces, or modify tracks.
 Filter enables classification by any statistics value (MeasurementPro).
 Statistics shows all the numbers, and exports them to Excel (MeasurementPro)
 Color moves your objects into the right light.
 Tools is the gate to your custom needs (ImarisXT)

Time Reduced memory overhead for a long time series, which consists of small 3d- or 2d-images.

File I/O New Reader: Nikon ND2

Surpass Camera New: "Center to Selection" moves the rotation center into the center of the selected object(s). This can be very useful, if an Object is selected by clicking on a value on the statistics tab, and the object is outside of the current view or obscured by another object. When rotating or zooming the camera, the objects stays in the middle of the view. This is may be also very useful to create accurate keyframe animations.

MeasurementPro
 Statistics Tab
Imaris 6.1 offers a completely revised Statistics handling to conveniently process your data for further analysis. There is a new Tab which displays all the values of the selected Surface(s).


There are new tool buttons to
  • Configure the computed statistics values
  • Select an object by its numerical ID
  • Duplicate the selected object(s)
  • Export the selected sheet of statistics values (new)
  • Export all the statistics values

  •  Color Tab
    With the new Imaris 6.1 you can easily Color Code objects by statistical values.



    FilamentTracer
     Spine Detection
    FilamentTracer has been extended by the class of Spines. This allows more accurate tracing of Neurons. The segmentation into Dendrites and Spines can either be done automatically, or you can also manually select parts of a Filament and assign it as Dendrite or Spine.

    Properties
     Settings has new options to visualize Dendrites and Spines.
     Creation shows the creation parameters, and allows to rebuild the Filament.
     Draw lets you paint Spines or Dendrites (with AutoPath or AutoDeph)
     Edit lets you assign a selection as Spine or Dendrite.
     Filter enables classification by any statistics value.
     Statistics shows all the numbers, and exports them to Excel.
     Color has individual colors for Dendrites, Spines, Branchpoints, etc.
     Tools enables automated Spine dlassification (ImarisXT)

    Statistics
    With Imaris 6.1 the FilamentTracer opens a new dimension for analysis of neurons. There are a lot of new, very specific measurement values.

    Overall:
  • Area
  • Full Branch Level
  • Length
  • Number of Branch Points
  • Number of Terminal Points
  • Number of Spines
  • Scholl Analysis
  • Volume
  • etc.
  • Dendrites:
  • Area
  • Branching Angle
  • Length
  • Mean Diameter
  • Number of Spines
  • Orientation Angle
  • Spine Density
  • Straightness
  • Volume
  • etc.
  • Spines:
  • Area
  • Length
  • Mean Diameter
  • Min Diameter
  • Number of Branchings
  • Orientation Angle
  • Straightness
  • Volume
  • etc.

  •  
    The graph shows the number of intersections depending on the distance from the Soma.



    ImarisColoc
    ImarisColoc Time dependent Threshold.

    ImarisXT
    XTensions
    Filament Spine Classifier

    This Matlab-XTension classifies your spines into Stubby, Muchroo, Long, or Thin Spines. The classification rules can be adjusted by the user. In order to start the XTension build a Filament (with Spines), select the Tools-Tab, and press the "Classify Spines" Button.




    Filament Convex Hull

    This Matlab-XTension computes the envelope around a Filament. This enable measurements of the occupied space (e.g. Area or Volume).




    Connect Tracks (Surfaces / Spots)

    If you're doing analysis of cell division, you may use spots and track them with the autoregressive model. This tracking model does a very good job, if cells of consecutive time points don't overlap. But this tracking model can not compute biforcations. With this Matlab-XTension you can connect the beginning points of tracks with other tracks. I.e. the missing biforcations are computed.

    tracking with autoregressive model adding the missing biforcations

    Programming Interface
  • Added: ISurfaces
  • Removed: ITrack, ISurface, IVectorField
  • Extended: ISpots, IFilament, IDataItem

  • Parallel installation of Imaris 6.1.0 and Imaris 6.0.2 is now possible. After installation of both versions a specific version can be addressed. Please have a look at the following Matlab sample:
    % starts the last installed version vImaris = actxserver('Imaris.Application'); % starts version 6.0 (or earlyer) vImaris60orEarlier = actxserver('Imaris.Application.1'); % starts version 6.1 (or later) vImaris61orLater = actxserver('Imaris.Application.2');

    64 Fixed Bugs (since Imaris 6.0.2)
    ID Summary
    3005 Olympus FluoView: Imaris does not read time series (only one time point)
    2971 unable to load a tiff series named 'ZebraWT-60x-0.16-SPIM_TL0001_Angle000_Ch00_Plane0000.tif'
    2967 imaris does not recognize ome-tiff-file (created by imaris)
    2910 BPStitchDatasets.m distorts voxel dimensions
    2896 XTension "Normalize Time Points" does not work for 16-bit images
    2885 partial .ims.part file remains and causes crashes
    2884 Display is gray first time you change to wireframe
    2880 Draw - Manual Slicer jumps back to previous position
    2878 Zeiss LSM random pattern
    2877 Cutting a surface of a time series corrupts scene
    2876 Deactivated External Object crash when data is imported
    2873 Spots are merged after region growing
    2862 'all Equidistant' function fails if the first time point was changed before
    2858 Imaris reads 8 slices even though the tiff file contains only one slice
    2854 unable to read a time series of imaris 3.0 and classic files
    2850 It is difficult to read the Play Back State list on Mac
    2848 Light position 'Fix to dataset' not restored correct from scene file
    2841 ImarisXT documentation: thresholds wrong descriptions
    2840 Duplicate manual selected spots from Filter tab crashes
    2822 Tracks XTensions do not recognise selection
    2813 'colors' playback state misleading
    2789 Rebuild region growing only done on first region of interest
    2782 Certain STK files cause corruption when in the same file.
    2772 Mapped color editor: selection stuck on lowest intensity box
    2770 Spots filter list: top filter only editable if other filters deleted first
    2769 2D image takes too long and uses much memory
    2748 Unable to locate 'ImarisThumbnailExtractor.dll
    2702 Filen name of in Imaris opened dataset should be available in XT
    2611 Adding or deleting a filter is very slow
    2582 Snapshot with off screen rendering causes white volume
    2508 The scene open dialog is named '�ffnen' instead 'Open Scene'
    2443 Upper IsoSurface threshold can be set smaller than lower threshold
    2429 annotation / figure does not remember view
    2410 Volume Rendering after Shadow and ChangeDataType is messed up (Windows Vista)
    2401 Rename "Special Folder" into "Specific Folder"
    2399 Big snapshot have multiple navi windows
    2395 Frame shadowing does not work with navi window active
    2389 2D timeseries need a lot of RAM to load
    2380 Undocking toolbars (with external projector active) hangs Imaris.
    2367 When sort tab is clicked, the selection in the surpass tree is lost
    2326 Problems with 'Add Slices'
    2323 path to save movie file always defaults to "colorTables"
    2266 The borderlines of the oblique slicer are not drawn rightfully
    2238 Surface Objects created from Region Growing produces also small Garbage Objects
    2182 Return Edge Preserving Filter to Image Processing menu
    2020 external object load path always defaults to Imaris folder
    1998 file extension filter for external objects lacks ".vrml"
    1987 Tracks black unless Time Color switched off
    1952 Generate Filament for all time points
    1922 Error during splitting. Found negative volume object...
    1902 Snapshot in surpass above 2000x2000 pixels is halved
    1825 Micron sign on scalebar wrong
    1675 check-box for AR1 values not available in Statistics settings
    1623 Delete button must not delete entire filament
    1587 Blend slider moves to late to mouse position
    1503 Spot tracking export crashes Imaris / Excel
    1421 sometimes can't display Coloc ROI mask
    1275 Filter for *.lei files in file requester
    1180 Color of surface relative to mean intensity of object voxels
    1107 Snapshot file requester with default image name.
    1001 Define angle of orthoslicer
    891 Each time sort tab or statistics tab is clicked, or made active again by another means , values recalculate, even if nothing has changed
    764 Statistics tab has no vertical scrollbar
    645 Save stack as mpeg appends .avi extension to mpeg file

    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: CL, 08-MAY-2008

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