Imaris | Release Notes and Bug Fixes

Imaris 7.2.0 Release Notes

Welcome to the Imaris 7.2.0 release notes. Version Date: December 1, 2010. 
Please have a look to the Overview of Imaris Release notes for information about prior released features and fixed bugs.

[Imaris
[ImarisCell
[FilamentTracer
[ImarisTrack
[ImarisXT
[Fixed Bugs
[Feedback]
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Imaris
General
  • Save movie files
    • MGP, MP4, AVI, WMV, MOV, FLV, TIF
    • Key Frame Animation, Time Animation, Slice Animation
    • Windows AND Macintosh
    • 32-bit AND 64-bit
  • IQ Open File

    Clicking on the 'Open iQ' opens the Image Selection window with a list of images and image information. The button appears, if iQ (Andor Technology) is installed on the same system (if the button is not visible "Edit / Preferences / Loading" allows to configure the iQ image path).

    This dialog allows to search images by it's name. It also allows to sort the list of images by various criteria (name, date, size, etc). The same new "Image Selection" dialog is also available for the settings of LIF or LEI (or any other multi-image-format).
  • New file reader: Olympus Virtual Slide Image
  • Menu "File / Open in new Window" opens an image in a new Imaris window. This makes it much easier on the Mac to open an image in a second Imaris instance.
Surpass General

  • Undo / Redo
    • Components: Spots, Surfaces, Filaments, Cells
    • Tabs: Edit, Track Edit, Draw
    • Shortcut: <ctrl> + z (or from main menu "edit")
    • The Undo command reverses the last action, when necessary. It supports multiple undo actions (Menu: "Edit / Preferences / Calculation / History"), starting with the most recent one and working backwards in sequence. All actions in the Edit, Edit tracks, and Draw Tabs as well as the image processing can be undone or redone, respectively.
Surpass Surfaces
  • Surfaces double threshold

    In Imaris you can choose two filter values, a lower and a higher filter value. The two filter values separate the data into three regions: above the higher value, below the lower value, and the region in between. Objects with the relevant properties below the lower filter value and objects with the properties exceeding the higher filter value will be excluded, and only those objects with qualities inside the defined interval will be considered. I.e. the upper threshold creates a hole, if the image intensitiy inside an object is very bright.

ImarisCell
Creation
  • Cell Creation Wizard Fill holes in Cell and Nucleus
    Before Fill Holes After Fill Holes
    Simple threshold based segmentation of Cell or Nucleus can lead to fully enclosed regions (assume bright intensity near the membrane and lower intensity in the interior). These regions are mostly invisible in 3d-MIP. Only a cross-section reveals this holes. The new option allows to fill these cavities, and it is recommended to activate it. There is an essential impact to volumetric measurements.
  • Undo for Tabs "Edit", "Edit Track" (see Imaris)
  • Drift Correction (see ImarisTrack)

FilamentTracer
General
  • "Filament" turns into "FilamentS"

    The new Filaments component is no longer a container for one single Filament (with maybe multiple unconnected parts). It now reports the statistics per Filament and not per image. I.e. it allows multiple beginning points (one per filament). If an image contains multiple neurons, Scholl analysis can now be performed on all the cells using only one Filaments component. Etc.
  • Option to select one full Filament (in addition to "Point", "Segment", and "Branch")
  • New statistical values
    • Spine Neck Length
    • Spine Neck Min Diameter
    • Spine Neck Max Diameter
    • Spine Neck Mean Diameter
  • Statistical Annotations (requires InPress license)
  • Similar as for the Cells a "Fill Holes" algorithm is now performed in the creation wizard (before diameter calculation). This operation can not be changed by the user. It improves accuracy of the diameter calculation, which was badly influenced by noisy voxels that turned into small cavities.
  • Undo for Tabs "Edit", "Draw", "Edit Track" (see Imaris)
  • Drift Correction (see ImarisTrack)

ImarisTrack
General
  • Undo Track Edit (see Imaris)
  • Drift correction for Filaments and Cells. Previousely only Spots and Surfaces were supported (see Imaris 7.1.0 Release Notes).

ImarisXT
XTensions Fiji / ImageJ
  • Integrated Fiji/ImageJ functions in Imaris. Functions or plugins for Fiji/ImageJ are executed for the currently loaded image in Imaris. This seamlessly extends the image processing of Imaris by many publicly available functions (GPL).
  • The user has to first install Imaris and Fiji (or ImageJ)
  • Then the executable path for Fiji (or ImageJ) has to be specified under "Options..."
  • A set of pre-configured Fiji-functions are available immediately
  • The Fiji-menu in Imaris is fully customisable. Fiji has a lot more functions available which are not pre-configured with Imaris (because several Fiji-functions are not meaningful in the context of Imaris). Technically there is a Fiji/ImageJ-macro behind each custom menu entry in Imaris. "Help..." provides more information how to configure the menu.
  • Windows AND Macintosh (XTensions based on Matlab work only for Windows)

Fixed 106 Bugs (since Imaris 7.1.1)
808 DataItem::SetColor(1,0,0,0)' does not change the color dialog
864 Contour Surface exported as external inventor object has size 1 kb
1386 Neither IsoSurface nor Contour Surface can delete the outer limits of a dataset.
1394 Contour not centered if min coordinates of dataset not 0
1454 ALT key to switch to Navigate does not work.
1577 Write cursor does not appear when text field is clicked.
1673 Scalebar in gallery view does not remember its position
1868 Files with asian character in path can not be read
1933 Shadow does not work properly
1978 Image Processin functions do unintentional undo
2371 some double rendered blocks for 512 x 512 x 512 image in slice view
2384 Image Processing causes black textures at some zoom levels
2408 Normal Shading: channel colors swapped (for some nvidia graphics boards)
2460 Matlab-XTensions should be gray, if the ImarisXT-License is present, but no Matlab is installed.
2489 When the amount of channels is changed the keyframe animation is deleted without warning
2491 AVI files bigger 2 GB are corrupt
2507 Imaris does not warn about a not saved scene
2738 Black texture in slicer after voxel size adjustment
2938 Animation/QTVR: Light source is always fixed to dataset
3025 Orthogonal mode does not work in Keyframe Animation
3068 ImarisXT mVisible=true doesn't work
3099 Preferences - System does not report Vista x64
3109 entire STK series not loaded when exported from multi-position ND
3215 text in many dialogs is badly formatted (only mac)
3267 Animation-->Volume-->Shadow Projection-->Fix Lights Broken
3512 FT statistics have timeplot, if multiple timepoints are selected
3573 "100%" Button in Surpass sometimes doesn't work and corrupts zoom factor "-1, #IO"
3585 Keyframe animation not correct w/ Display Adjustments
3586 Keyframes get lost when applying Matlab functions to dataset
3628 Orthogonal + 100% = Weird perspectives
3651 Calling "AddSurface" from ImarisXT does not work for individual time points
3655 Filter only works on first time point
3779 Quicktime not working with Imaris x64 (Win and Mac)
3819 Some Surpass Tabs have no context help
3950 New Contour Surfaces Broken with Default Keypress rate on OSX
4017 .iv file crashes Imaris for Mac
4151 compressed AVI options don't work on Win32
4153 Cut surfaces leads to random crashes
4154 Cut surface does not cut in the correct area
4218 Extended Section View broken for both Ortho/Oblique slicers
4242 IPSS license does not prevent Matlab functions from appearing
4273 Save as function hangs when Imaris is closed or new file opened
4290 Surfaces creation does not update channels list after dataset changes
4326 Formula for Spot Speed wrong
4357 Olique Slice position changed automatically during animation
4360 Floating License being denied with two active IP address
4435 Failure to load Imaris - Crash on load
4451 Andor images with pseudo-color are not loaded properly
4470 Histogram is the same for every time point
4478 Nucleus Number of Vesicles Value wrong
4523 Resample open, subsample X by 5 causes Immediate crash
4535 Track connection to spot on same time point is drawn
4536 fixed time indicator not updated
4542 The Selection of track edit not updated when the connected tracks are selected by clicking a track
4546 Cancel surface creation wizard ater segmentation, and then "play time" crashes Imaris
4547 Message in Crash-Reporter regarding failure to get graphics board name is missleading
4551 Spots Rebuilt crashes Imaris with ImarisXT Matlab Com interface
4554 no output files generated for surfaces and cells (only spots works)
4558 Online license: multiple hostIDs: click OK without selection -> crash
4570 Wrong sequence in documentation for filament and surfaces creation
4572 Rotational and translation drift correction crashes Imaris
4574 Clipping plane orientation not used in animation
4577 Open dataset from dir with Chinese characters in root dir crashes
4579 Import Spots to Cells crashes
4588 Can not write to folders with French characters
4594 Can not export Cells, Nuclei or "full export" with ImarisCell object with multiple timepoints
4597 Contour crashes after "undo", if contour was not closed
4599 OmeTiff written by Imaris are not recognizedas Tiff
4600 Opening Ome Tiff files from Till Photonics crashes Imaris
4613 Opening some Zeiss 700 lsm file crashes Imaris
4617 missing frames 3D stack #63, #125, #187 in Imaris 7.1.1, but not Imaris 7.0
4623 Black layers on selected zoom levels in the middle of the dataset
4624 Creation parameters for Threshold Algorithm not stored
4625 Extreme bleftness jump during zoom of inverted dataset
4629 Keyframe lost animation when Coloc adds a channel
4633 spine neck calculation problematic
4636 .ipl IPLab 3D timeseries does not open properly
4646 Surfaces "Ellipsoid Axis A" has same values for X and Y
4650 License Checkout/Checkin in wrong order
4704 Volume + Orthogonal Camera + 100% = Image Block Disorder
4736 Classify spines Xtension needs an Starting point to work
4741 Crash when going back and forth between Classify Tracks and Complete ROI
4746 Contour crashes drawing Circle after Distance mode
4758 Transparency slider on color tab not updated, when keyframe animation is played
4764 file settings dialog opens always the iQ image folder, instead of the selected LIF-file
4766 Manual does not list . , as an alternative for changing width of contour line
4770 compiled XTension "attenuation correction" does not work
4776 Content of color tab is missing when loading an .iv file
4777 Imaris crashes when selecting the statistics tab of an "empty" volume
4800 Cell masks are displayed in wrong time points.
4806 Imported Spots invisible by default
4807 Cells transparency should not affect rendering in MIP mode
4808 Camera Manager XTension requires admin lefts
4809 Object Manager XTension requires admin lefts
4810 MCR + Intensity Line Profile Crashes
4822 Imaris crashes when I use Cell Module
4831 Bleft blocks in volume rendering and strange histogram after filament calculation
4832 BMP saved in matlab causes memory leak in Imaris and crashes computer
4841 XT tool for classification of spines stops at 50%
4866 BatchAgent (Set Coordinates ) does not work, and does not set voxel spacing.
4868 Cells crashes with defaults on specific dataset
4873 ImarisCell crash in 64 bit mode at step 3/6 in wizard
4874 ROI used in wizard, but no ROI is selected...leads to Imaris crash/shutdown
4879 The more region of interests the lower the automatic threshold for surfaces
4888 IQ 2.1 DiskFile + Thumbnails --> Crash
4893 Mean Intensity of a surface filled with intensity 255 is 255,953

Feedback

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

Last Modification: CL, 18-Jan-2011

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