Bitplane | Release Notes | Imaris 8.4

Imaris 8.4.0 Release Notes

The main feature of Imaris 8.4 is manual filament tracing for large images. Both Autopath and Autodepth tracing are improved significantly in this version to enable filament tracing in large images. The following is a list of all the new features of the Imaris 8.4 release.

ImarisFileConverter
ImarisFileConverter is big data capable. It easily converts terabyte sized files from almost any microscopy format or from tiff-series to the high performance IMS format that allows immediate interactive visualization of terabyte sized images.

In version 8.4 we have made ImarisFileConverter more responsive with better progress updates and a more interactive user interface. Here is a screenshot of the new User Interface.



The top table of the user interface is the input area which allows users to set up the list of files to convert and to configure the settings of each file before they start the actual conversion process. When a conversion is started by pressing “Start All” files are moved to the bottom table which displays the progress on the running conversion.

New in ImarisFileConverter8.4
  • Both read and write progress are displayed.
  • Conversion runs in a separate process (ImarisConvert)
  • It is possible to add new files and configure settings while a conversion is running.
  • Number of threads for conversion is configurable
  • Output format is IMS 5.5 only (removed 3.0 and 2.7)
  • Preferences FilePath removed because conversion does not require page files.
  • File Series Settings allow to specify voxel size
  • Default Memory usage increased to work with big images
Filament Drawing Autopath
Autopath filament drawing is big data capable.
  • Autopath calculation runs in separate thread.
  • Users can start tracing immediately after placing a start point.
  • The size of the cursor determines the resolution at which the tracing is calculated (larger cursor => lower resolution => faster calculation and less precision but often the low resolution paths are surprisingly good.). Users can develop a sense of the effect of the cursor size.
  • Channel drop-down lets user specify the channel on which the calculation runs.
  • Placing a new start point cancels the previous calculation and starts again from the new start point.
  • Preferences FilePath removed because conversion does not require page files.
  • Interaction:
    • "Shift+Right-click to start."
    • "Shift+Left-click to add path."
    • "Shift+Ctrl+Left-click to add path and restart."
    • "Shift+Ctrl+Right-click to connect and restart."
    • "Hold Shift to activate autopan."
  • Shift+Ctrl+left-click adds a path and restarts the calculation from the current position making it very easy to trace a path in multiple small steps.
  • When a start point is placed close to an end point the path will automatically connect.
  • The most recently drawn filament is automatically highlighted.
  • Pressing Ctrl+8 is useful immediately after adding a path to turn on InMotion for validation of the tracing.
  • Checking the “AutoCenter” checkbox runs an automatic centering when the path is added (after pressing shift+left-click).
  • Checking the “AutoDiameter” checkbox runs an automatic diameter calculation when the path is added (after pressing shift+left-click). The calculation takes the mouse cursor size on shift+left-click as an input parameter (initial guess of diameter). The mouse cursor size should roughly correspond to the diameter of the filament for the calculation to succeed.
  • Autopath mode respects clipping planes: It chooses start and end points only within the visible part of the volume. The view section of the draw tab lets you move the near clipping plane of the camera to clip away things that are close to the camera and it lets you specify the thickness of the visible region.



    Note: Be careful not to clip away parts of the filament that you are drawing because this can break the drawing.
Note: there is (unfortunately) no visual indication of the progress of the autopath calculation. The only way to find out is indirectly from moving the mouse pointer to different positions in the image. For those positions where the calculation has already arrived a tracing will be shown. For those positions where the calculation has not yet arrived no tracing is shown. Note also: Since it is very easy to trace a small piece and then continue the tracing from there users can work without interrupt.
Filament Drawing Autodepth
Autodepth filament drawing is big data capable.
  • Autosnap makes drawing easy. The user does not need to keep the mouse pointer exactly centered on the filament structure because it autosnaps to the nearest filament structure.

  • The size of the autosnap region is proportional to the 3D cursor size.
  • When ambiguities arise autodepth keeps track of multiple paths until the ambiguities resolve. (Only the best is displayed to the user).
  • To draw in autodepth press shift+left-click. You can release the shift key after you started drawing. The segment will be added to the filament when the left mouse button is released.
  • Pressing the d-key on the keyboard while drawing enables an eraser. You can now draw backwards to erase parts of the filament. This works only on those parts of the filament that were drawn right before pressing the d-key.
  • Torch highlighting helps to focus the user’s attention in 3D.
  • Autopan allows to draw along filaments that extend out of the initial view because the view starts to pan when the mouse approaches the border.
  • Shortcut Shift+T toggles between Torch View and Full View.
  • When a start point is placed close to an end point the path will automatically connect.
  • The most recently drawn filament is automatically highlighted.
  • Pressing Ctrl+8 is useful immediately after adding a path to turn on InMotion for validation of the tracing.
  • Checking the “AutoCenter” checkbox runs an automatic centering when the path is added (after pressing shift+left-click).
  • Checking the “AutoDiameter” checkbox runs an automatic diameter calculation when the path is added (after pressing shift+left-click). The calculation takes the mouse cursor size on shift+left-click as an input parameter (initial guess of diameter). The mouse cursor size should roughly correspond to the diameter of the filament.
  • Autodepth mode respects clipping planes: It chooses start and end points only within the visible part of the volume. The view section of the draw tab lets you move the near clipping plane of the camera to clip away things that are close to the camera and it lets you specify the thickness of the visible region.



    This is useful in large images where structures occlude each other. Note: Be careful not to clip away parts of the filament that you are drawing because this can break the drawing.
Note: Because of autosnap it is important that the cursor size roughly matches the diameter of the filament that you draw.
Snapshot
The snapshot button in the main toolbar immediately produces a snapshot of the current view. By default, the snapshot is saved to a file in the source image directory and after creating the snapshot it is opened in the default image viewer to show the user what the snapshot looks like. The snapshot is by default also copied to the operating system clipboard for use in other applications. Users can modify the behaviour of the snapshot button by changing the snapshot preferences:



When the Scale value is set to 1 the snapshot button creates a snapshot with the size of the render-area. To create high resolution snapshots, the user can change the “Scale” preference to a value larger than one. If the Scale value is set to 2 the resulting snapshot will have 2x the width of the screen render area and 2x the height of the screen render area.

To help the user see the size of the screen render area Imaris displays this size in the top left hand corner of the render-area whenever the size is changed.



Also the view-menu now has the possibility to “Save Window State” and “Load Window State” which functions on a per viewer basis and saves and loads the size and visibility of all windows.

Note: Snapshots always have the same aspect ratio as the render-area of the current view. In previous versions of Imaris it was possible to create snapshots with aspect ratios differing from those of the current view.
New Navigation Control in Surpass-3D View
  • Zoom to Cursor: The point under the cursor remains under the cursor while you zoom. This is extremely helpful when you want to zoom to a specific location. With Filament Autopath and Filament Autodepth tracing at very high zoom levels this behaviour is extremely valuable.
  • Rotate around visible part of the image/scene: The center of rotation is in the center of the visible part of the image/scene. This leads to images remaining in view better during rotation.
  • Zoom through image: It is possible to zoom all the way through an image to the other side. This is very useful when the point that you want to zoom to is close to the rear part of the image.
  • Fix Center: Click the Fix Center checkbox to set the center of the 3D cursor position so it will rotate about this point even it the image object is moved within the image viewing window. Note: You can press the shortcut key F6 when the 3D cursor is visible to perform this function (the Fix Center option in the Camera panel gets checked). This shortcut key will have no effect when the 3D cursor is not visible.
For those users who prefer the old behaviour of Imaris it is possible to change back to the old behaviour in the Preferences Display section.

Note: The functionality of “Set Center” in the 3D-view camera toolbar is affected by this new behaviour. While Set Center will reposition the camera to the same position as in previous versions the focus point around which the camera rotates is changed with the zoom of the camera (in order to allow to zoom through the dataset).
Graphics Memory Autodetection
The preference for Display::TextureCacheLimit is automatically determined from the available memory of the graphics board when Imaris is used for the first time.
Display Adjustment improved Auto function
The Auto setting of the display adjustment is improved.



The calculation now works as follows: The minimum value is set to the first mode (maximum) of the histogram. The maximum value is set to a value that is around the 99.8 percentile of the histogram which effectively disregards high intensity outliers.

Scalebar Position and Size
Scalebar Position and Size can be adjusted in the preferences:

Old Zoom Definition
100 per cent maps one voxel to one screen pixel in any of the views.
Parallel Spots Statistics Calculation
In Imaris8.4 the calculation of spots statistics is multithreaded and blockwise.
Renaming of some function in Cells Edit Tab
On the Cells edit tab the function “Merge” is renamed to “Fuse” and “Split” to “Fragment”.
Possible to change color of Vantage 1D plot
Added a color wheel icon that allows changing color of each Vantage 1D object.

Statistics “Track Intensity Median” definition changed
To improve statistics calculation performance the definition of the “Track Intensity Median” Statistics is now:

Track Intensity Median = Average of all Intensity Medians of all objects at all time points in the track

In previous Imaris versions the Track Intensity Median had computed the median of all voxel intensities within all objects at all time points within the track. This operation required visiting image intensities. With the new definition it is possible to calculate the Track Intensity Median statistics from the already calculated Intensity Median voxel statistics for each object.
Exact Distance Transform
The distance transform calculation is an exact distance transform computed using the method of Meijster, Roerdink, Hesselink: “A general algorithm for computing distance transforms in linear time”in Mathematical Morphology and its Applications to Image and Signal Processing, Volume 18 of the series Computational Imaging and Vision pp 331-340.



The exact distance transform is used throughout Imaris8.4 wherever distance transform calculations are done. This leads to differences in statistics values like “vesicle distance to cell membrane”. Also the results of some of cells, surfaces, spots and filament detection may differ due to the changes in the distance transform.

The exact distance transform is also applied when distance transforms are run via ImarisXT.
New Filament Spine Statistics
Filament has 3 new statistics values:
  • Pt Spine Total Length = total length of spine starting at this spine attachment point.
  • Pt Spine Total Area = total area of spine starting at this attachment point.
  • Pt Spine Total Volume = total volume of spine starting at this attachment point.
Easier access to some functions on Filament Edit Tab
In previous versions Filament Edit Tab, there are three functions which need Source Channel Selection: Center, Diameter, and Join. Also, the function Diameter need other three input parameters: small diameter, large diameter, and threshold value. We streamlined the dialog in order to avoid the popup that was needed and integrated it directly in the edit tab.

New Reference Frame Manipulators
Reference Frames can now also be positioned using visible manipulators:



Also, as shown in this screenshot the reference frame axes have labels in the 3D scene.
Supported Operating Systems
Imaris8.4 is supported for Mac OS X 10.9 and higher.
Imaris8.4 is supported for Windows 7 x64 and higher
95 Bugs Fixed in 8.4
9716 Using the quality filter in membrane detection when no Cells are detected will cause a crash
9694 Editing a Filament with loops causes the Save/Export to fail
9683 Rebuild of Spines activates ROI
9651 Incorrect opening of >2 gb Fused CZI tiled images
9648 Crash on Filament Join...
9645 Memory Limit Accepts Negative Values
9631 Batch for Filaments fails on all datasets
9628 Region Growing Slicer Position is Reset when changing threshold value
9621 Truncated names in Arena when selecting objects for manual collections
9625 Reference manual Missing description/diagram of Velocity Angle statistic
9608 Disabling Interpolation has no effect
9602 Batch fails on group of files for all the files
9586 Cells wizard crashes when settings tab is open and you click into rendering area
9578 Opening successive lsm files on mac will crash Imaris
9559 Undo does not work for extract channel
9558 Building Vantage Plot uses lots of RAM and takes virtually for ever
9555 Cannot run successive XTensions on OS-X
9551 Batch Queue is still enabled in file menu when the batch licence is not present but pressing it has no effect
9542 Imaris cannot open 1.2TB SPIM dataset used previously for huge data tests
9538 Time stamp in OME-Tiff not read
9526 Imaris crashes when free rotating a data set
9525 Animation TIFF export jumps to first time frame in last keyframe
9524 filament statistics are doubled
9518 Imaris crashes when opening a coloc data set and the license is not available
9509 Clicking on the Cylinder track style crashed Imaris
9505 ObjectIds of Tracked Cells change after store and load
9502 Contour drawing mode 'Time' stops when new circle on same frame is started
9495 The distance values in the 3D crop window should be closer to the corresponding pixel values
9489 Reference Frame is listed as product Reference Frame instead of Imaris MeasurementPro
9483 Extract Channel adds channel with improper dimensions
9481 Data not saved when Arena is off and Imaris gets closed
9470 Filter Dialog loses Filters after Duplicate Selection
9464 Added Tags in Arena are lost/deleted if user moves/duplicates file to a new group
9458 Visualization of objects in Vantage while only showing labelled objects differs between object rendering and center point
9457 Order batch results by file name rather than by completion time
9456 Cells Membrane Threshold entry for Creation Wizard missing from reference manual
9453 Using Multiple filters is broken, in both Creation wizard and in regular filter set.(affects surfaces, cells, spots, filaments)
9443 More sensible locations for file export and open dialogs to default
9438 In version 8.3, upon Build Coloc Channel, No statistic is generated
9437 Transparency of Shaded Volume Cells is too limited
9431 About Dialog in Imaris Administrator should have its own window
9428 Help for Programming Interface - Broken Link
9421 Adding multiple Spot/Cell objects disables the Filter Dialog.
9407 Imaris crashes when I try to delete 16 segments in Filaments
9387 Resample Image to align Reference Frames button should be inaccessible in single time point image
9383 Imaris provides no indication of which axis is which while using Reference Frame
9378 Imaris uses "Merge" and "Split" for two very different actions in Spots/Surfaces as compared to Cells
9351 Switching between 'Create' tab and 'Settings' show more Seed Points than selected
9317 Switching between manual filament and AutoPath or Auotdepth fails to remember postions
9316 Filament classify spine statistics - Average stats only showing Stubby spines.
9306 Search tool in Annotation crashes Imaris
9304 Add image folder throws warning for files which are associated with an image file
9243 Datasets opened through Fiji/File/Open retain the file name of previously opened files
9242 Manual Autopath can not trace filament in one go while wizard Autopath does
9181 If Imaris can not reach the floating license server you get stuck in splash screen
9168 Volume display is blank after deleting 1 or more timepoints from original ND2 file.
9130 Frame number overlaps time values on the timebar for OS-X
9109 Editing filaments removes all labels
9101 Volume statistics get "lost" if time series is cropped
9095 With 'Object' selection mode active in the track editor clicking on a track in the rendering area will highlight nothing
9093 Cells object (without vesicles or nuclei) cannot be exported for plotting
9074 Update text for 'Off Screen Rendering'
9064 Dataset with millions of spots causes crashes in 'Edit Tracks' and 'Statistics'
9058 Rebuilding Surfaces after editing a lineage track takes too long
9053 Editing Lineage tracks then going to the Color Tab stalls during statistics calculations
8973 Track Editor's bottom scroll bar behavior is different from right scroll bar behavior
8943 BatchAgent doesn't clean up temp files from failed batch runs
8647 filament should be displayed as line during rebuild process
8644 Names for Surpass objects created in 7.6.5 do not display in Arena
8600 Filament cylinder size set by default to 1000um in CZI files
8498 Contour time drawing frequency not set
8310 Default rendering style of Filaments from a batch run is line while from the wizard is cylinder
8189 OME validation scripts generates errors for OME export
8089 Coloc unstable when no dataset is loaded
8088 Exporting annotation when no dataset is loaded crashes Imaris
8020 You can not have the scale bar in the lower half of the gallery
8016 Classify Spine XTension does not work for all datasets with recent Matlab versions
7979 Adding manual Spots/Filaments with no volume data causes a crash
7925 Rebuild filament leads to additional entries in the statistics which are zero
7895 Coloc panel appears when Snapshot is activated from Surpass mode
7781 Some ome-tiff files are not read in correctly
7774 XT can access invalid data while background loading is active
7747 Olympus Tiff saved by VS-ASW 2.5 (Build 9483) wrong XYZ calibration imported
7536 Statistics Calculation for spots is slow compared to 7.6.5
7467 Filament Rebuild All does not produce the same results like a fresh build
7301 False/Misleading count display in "Selection - Average values" of the Statistics tab
7108 Spine count varies between Imaris statistics and Matlab Plot if count=1
6904 Snapshot output does not match preview of overlays (e.g. scale bar units)
6636 Add workflow to automatically detect spines on manually traced filament
5969 New OME files not properly read (reader and writer outdated)
4149 Scalebar / Color bar label does not scale with snapshot size
3525 Part of spines still visible when 'Show Spines' is off
3462 Volume is not shown on load after surface or filament wizard started
3263 Improve Duplicate Filtered Object Behavior
2417 Snapshot of gallery mode is not properly imaging the preview
12 Feature Requests Implemented
1973 Option to set behavior of default snapshot path
4016 Imaris should support saving external objects as .WRL file type
4352 FR:Autodepth Cursor Placement should be aware of clipping planes
6397 No Crosshairs should be visible in a Snapshot of Section view
6564 Snapshot widget forgets previously set filename
7675 >2 gb Fused tile CZI image file does not open in Imaris (Imaris opens the fused tiles incorrectly)
8601 Bring back the old Zoom value behavior
8803 Cannot load (new) OME-XML files supplied by customer
9362 Customer wants only "m:ss" time display in 3D View
9364 Name of Statistic value not added to Excel export
9620 Cannot change 1D vantage graph color
9633 Default tab of 'Imaris Administrator' should be 'License' after installation
Feedback
Any feedback on the installation, and the usage of Imaris and its features are welcome. Please send your comments to eusupport@bitplane.com

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