Imaris | Release Notes and Bug Fixes

Imaris 4.0.3 Release Notes

Welcome to the Imaris 4.0.3 release notes. In this version we have changed the configuration of Imaris and introduced a lot of key features. Version Date: AUG 22, 2003.

[New Tracking] [New Measurements] [New Configurations] [Core Features]

New Configurations
Imaris
Imaris Becomes More Powerful!

As of this version we have integrated all the features, except for measurements, of what we previously called ImarisSurpass into the core Imaris. The term ImarisSurpass has disappeared. We refer to the functionality as "Surpass view" in Imaris. The measurement features of ImarisSurpass have been integrated into ImarisMeasurementPro.

We have also included all our highly specific file format readers into Imaris. Users who owned a partial file reader set will be receiving the full set of licenses with this upgrade.

ImarisPersonal

Imaris Becomes Affordable!

We have newly released ImarisPersonal. This product includes the file readers, image processing functions, and classic viewers of Imaris (outline in read in the toolbar below).

ImarisPersonal addresses two user groups: (a) labs with a limited software budget, and (b) satelite users of an imaging facility running the full Imaris suite.

The following restrictions apply to ImarisPersonal:

  • There is not maintenance program available. Users who wish to upgrade their ImarisPersonal need to buy a new copy from time to time or cross-upgrade to Imaris.
  • ImarisPersonal cannot be combined with any of the modules (e.g. ImarisColoc). Before adding modules the ImarisPersonal license needs to be upgraded to Imaris.
  • There are not floating license schemes available for ImarisPersonal. This product is always licensed for one computer (i.e. node-locked ).
ImarisFreeware

Imaris Becomes More Available!

We have added the Section and Gallery views to the freeware mode of Imaris which now includes the following features:

  • slicer, section (including MIP and blending projection of extended sections), gallery
  • read images in Imaris, ICS, Tiff, and BMP format
  • add/delete channels
  • resample image (change resolution)
  • change data type (16- to 8-bit)
  • save as Tiff, BMP, ICS files
  • view image parameters

New Features since last Version

The tables below lists all new features and bug fixes of Imaris 4.0.x in comparison to Imaris 3.3.2.

Imaris Core (including Surpass view)
SurfaceObjectc []

A new objectwas added to Surpass and was named SurfaceObject. It was formerly referred to as "split IsoSurface" because - unlike the IsoSurface - it contains only one closed surface. SurfaceObjects are derived either from IsoSurfaces or from a set of contours (see below, the latter requires MeasurementPro).

Because of improvements realized in algorithm design and data management and because of the smart calculation of intensity statistics the creation of SurfaceObjects have been accelerated by a factor of 10!

IsoSurface []
The IsoSurface object has become more dynamic and recomputes whenever the user changes the current time point or makes alterations to the volume image (channel) from which it was computed.
Movie-Export

Imaris supports new formats to export animations time series movies:

  • AVI
  • MGP
  • TIFF files
Besides these additional formats the user can now specify the frame rate and - for some formts - the compression rate.

New file formats supported:

  • Olympus Biosystems cell^R
  • Biorad confocal time series images.
Drag and Drop (DND) behaviour in the Surpass component list has been improved and provides more visual feedback.
Filtering A new filter function has been added. This function was known from our NeuronTracer before and is now available in Imaris. It takes two thresholds. Voxel intensities below the lower threshold are set to 0, voxel intensities above the upper threshold are left unchanged. Voxel between the two intensities are set to 0 unless they are "connected" to a voxel above the upper threshold. Connected means that there is a unbroken path of neighbors and neighbor's neighbors which finally ends at a voxel above the upper threshold. Location: ImageProcessing : Noise Reduction : Connective Baseline
Progress bar has become smarter and avoid flickering with very frequent updates.
License

The license dialog has been re-designed to allow deletion and modification of previously defined license information.

Imaris will check for licenses of higher version and inform users that a newer version of the program is available on the server.

 

ImarisMeasurementPro: Updated Statistics
Statistics for Additional Components

A statistics tab is available for the following components:

  • IsoSurface
  • ManualSurface (contour based surface)
  • SurfaceObject
  • Track
  • and Group (only if the grouop contains any of the above objects)
Unified Statistics Display

The display of statistics has been unified in the entire Surpass view.

The statistics viewer support selections of cells (CTRL-A for all cells) and copy to the clipboard. A new feature allows to transfer the statistics data directly from Imaris into Excel.

Statistics is now computed only when the user switches to the statistics tab. This increases the performance when creating SurfaceObjects and IsoSurfaces.

The display of measurements has become context sensitive. The statistics tab in the property windows of Surpass displays different information depending on which object (or group of objects) are chosen.

 

Tracking is not an individual ImarisModule. It is a set of features which become available if the two modules ImarisTime and ImarisMeasurementPro are installed which makes it available to all users with these modules under maintenance.

New Tracking Subsystem
ROI measurement over time. Newly introduced intensity measurement of arbitrarily shaped regions (ROIs) over time. The ROIs are created as a manual surface (requires MeasurementPro). Such SurfaceObjects are then copied to all time points and the corresponding intensity measurements are displayed on the user interface nad exported.

Tracking

ImarisTime + ImarisMeasurementPro

Users who have the two modules ImarisTime and ImarisMeasurementPro under maintenance will get the new tracking subsystem at no extra charge.
Track Object [] Imaris offers automatic tracking based on the identification of SurfaceObjects in consecutive time points.
  Tracks can also be created manually by stepping through time points and picking SurfaceObjects which belong together. This process is accelerated through the combined use of arrow keys and mouse.
  Objects can split and merge which causes the tracks to branch.

An interactive TrackEditor allows users to create tracks manually or modify tracks which have been created automatically:

  • create links between objects (or entire tracks) that belong together but don't segment in one of the time points
  • remove unappropriate branches
  • split one track into multiple tracks by removing a central connection
  • extend tracks with SurfaceObjects that use a different threshold

 

This figure shows the track editor with a simple track. The track is mostly linear. At time point 2 there are two objects which originated from one object in time point 1 (split).

Tracks are visualized in multiple ways:

  • All SurfaceObjects of one track can be colored alike (blue, orange, and red have been used below).
  • Trakcs can be hidden, shown as line, as cylinder with uniform diameter, or a cylinders with a diameter being proportional to the volume of the SurfaceObject at that time point.
  • The time can be color-coded onto the tracks (in the figure below blue indicates time point 1, white indicates the last time point).

Auto-Coloring Tracks and SurfaceObjects

By selecting multiple tracks as lines and with the time color-coded onto the track it is possible to visualize a motion field. The lines represent the center of mass of each of the SurfaceObjects at early (blue) and late (white) time points. The color of the SurfaceObjects is automatically derived from the channel color.

  It is possible to create an IsoSurface only for one time point in a time series images. This allows the user to choose different IsoSurface thresholds for differnt time points to optimize the classification and segmentation of objects.

 

Bug Fixes
Imaris Olympus last layer channels are mixed up. [459]
  Crash with Zeiss Axiovision ZVI version 4 [450]
  Imaris crashes on opening if no valid license [415]
  Date/Time not saved in Imaris 3 file format [476]
  Keyframe animator writing MPG files at a rate of more than 50 frames per second crashes Imaris [429]
  SurfaceObjects do not disappear after split, reduce or manual surface as we move to different time point [357]
  STK format: calibartion and date not read correctly [424]
  Leica time series crashes Imaris [509]
  Cannot Load Biorad 2-channel time series [493]
  Two channel single slice Olympus data sets not read correctly [475]
  Biorad 2channel with different filesize, only first channel is loaded [468]
  Only first slice of Biorad time series are read [517]
  Resample z for 2D images crahes Imaris [516]
 

Split of IsoSurfaces which are invisible may actually split an IsoSurface at a different time point [514]

  Imaris BMP reader could not load images previously written with Imaris BPM writer [510]
  Zeiss LSM410 images loaded too slowly [504]
  If Imaris was started by doulbe-clicking on an Imaris file or by launching from ImageAccess the ImarisColoc windows was not initialized properly [501]
  Metamorph 4D image series read out of sequence [496]
  The adjustable TIFF series loader crashed Imaris for certainl filter settings [490]
  LSM410 look-up table was loaded instead even if the loader preference was set to the "default colors" [464]
  If multiple key frame animations are generated it may happen that Imaris crashes reporting a write protection failure [458]
  The crop3D rubber band selection jumps when the mouse was initially clicked making it difficult to adjust the crop area [431]
  Fly-through in Full3D does not work properly [413]
  Zeiss Axiovision look-up table not loaded [253]
  Wrong recent file entries in File manu after saving file series [220]
  Cannot remove license entry for floating server [255]
  Contour statistics lost after triangle reduction [471]
  Track Property Dialog Inactcive After Loading Scene [512]
  Volume calculation was off by factor of 2 in version 4.0.2.
  Imaris crashes with certain Olympus cell^R files.
ImarisColoc Coloc crash when entering a value below data range [508]
  Coloc 2d histogram does not react to threshold- or channel-changes [507]
  Channel color does not update in Coloc if channel color is change [379]
  Automatic thresholding in Coloc crashed Imaris for time series images [512]

Feedback

Any feedback on the installation, and the usage of the Beta products listed above are more than welcome! Please send your comments directly to the product management(messerli@bitplane.com)



Last Modification, ,  MM 29-AUG-2003

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