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Imaris 9 Release Notes

Welcome to the Imaris 9.0 release notes. Please have a look to the overview of Imaris Release notes for information about prior released features and fixed bugs.

Version Date: July 18, 2017

Surfaces capable of “Massive Model Rendering”

With Imaris9 it is possible to interactively render surfaces of 100GB size or larger. Exactly as Imaris’ proven volume rendering technology this new surface rendering technology is based on a multi-resolution octree. The following rendering shows a surface with blocks at different resolution levels.

With this technology Imaris9 can render interactively massive surfaces consisting of billions of triangles.

The technology that enables fast rendering of large surfaces is based on the following features

Fast Surfaces Computation

To compute surfaces from large images efficiently Imaris9 runs blockwise and multithreaded computation of surfaces. The computation uses system resources efficiently. The computation of surfaces from a 100GB image will still take hours to complete but a) it is possible and b) the computation is faster than in previous imaris versions despite the fact that in Imaris9 surfaces need to be computed at many resolution levels to facilitate fast rendering.

Surfaces Performance

Performance tests show that Imaris9 computes surfaces almost an order of magnitude faster than Imaris8.4.1.

Surfaces Render Option “Slicer”

In Imaris9 surfaces can be rendered on a slicer (ortho or oblique). This is a valuable tool to compare the segmentation to the original data.

Surfaces for 2D Images Automatically Render in Slice View

Imaris9 is the first Imaris version that natively renders 2D surfaces as 2D. (Previous versions of Imaris computed 3D surfaces from 2D images.)

Blend Mode Transfer Function

In Imaris9 the Transfer Function for blend rendering is adjusted in a user interface on the settings tab of the volume component. The Transfer Function determines the opacity (transparency) of voxels by mapping intensity to opacity. The transfer function is displayed as a graph overlayed onto the histogram of the channel intensities. The vertical axis depicts the opacity value. Values at the top of the graph are completely opaque. Values at the bottom are completely transparent.

The transfer function can be changed by dragging the control points in the transfer function editor or via numeric entry fields for more accurate positioning when comparing across different files. Clicking on a line allows to shift the transfer function left-right.

Changing Display Adjustment Changes Colors

Changing the Transfer Function Changes What is Rendered

Transfer Function is stored in IMS

The Transfer Function settings are stored in the IMS file separately from the display min/max.

Blend Mode Automatic Settings Improved

Imaris9 has an improved auto adjust functionality that is available on the volume settings tab in blend mode.The improvements are two-fold. The new function is faster and it produces better results.

Normal Shading Mode Automatic Display Adjustment Improved

Imaris9 has an auto adjust functionality that is available on the volume settings tab in normal shading mode.

Ctrl+Right Click on Color Bar in Display Adjustment Performs “Auto” on One Channel

Because the “Auto Adjust All Channels” button adjusts all channels it is sometimes useful to use this shortcut to auto adjust only a single channel.

Fast Save of Changes to Display Adjustments

When the user opens an image and changes the display adjustments and then decides to save those changes old versions of Imaris took quite a long time to save the changes. In Imaris9 this is a matter of seconds.

Histogram Zoom

The histogram has a zoom bar at the top. Mouse wheel allows to zoom in and out. Holding right-click on the zoom bar allows to pan. Double right-click resets the zoom.

Lineage Tree Graphics Export

The lineage tree can be exported either as SVG vector graphics or as a high resolution tif image to facilitate import in other software to prepare publication quality graphics.

Snapshot to Predefined Size

The user can specify a snapshot output width and height in snapshot preferences.

In order to get a good preview he/she can choose from the snapshot dropdown to render the window in “Fixed Size” which then results in the viewport getting the same aspect ratio as width/height of the snapshot so that he/she can easily preview the result (at screen resolution)

H264 Video Codec

Imaris9 videos saved as MP4 will be saved using the H264 compression codec. Alternatively they can be saved as Raw or as tiff series (all other options were removed to simplify the UI).

Automatic Settings/Preferences Migration

System preferences are automatically migrated during installation of Imaris. User preferences are automatically migrated on first start of Imaris.

New File Readers

File Reader Plugin Capability

Imaris9 searches the filereader plugin directory for DLLs that have the FileReader API. When such a DLL is found it will be added as a filereader to Imaris.

The API supports both readers that read (contain) just one resolution level as well as readers that allow to read multiple resolution levels. In the latter case it is possible that Imaris renders files opened through a reader plugin in native mode (without reading the entire file before rendering).

Fixed Bugs

Bugs fixed in 9.0
5038 Coloc ROI histogram does not update after changing Channel selection
5318 Mask generates corrupt channel with horizontal stripes
7147 Problems with .mov and .mp4 movie types with less than 6fps
7652 Wavelength not read from CZI file
8658 Surface rendering fails on huge XY image
8703 Crash after taking several snapshots in a row for larger time series
9066 site.cfg file corrupted
9354 Adding multiple LIF files by "Add time points" gets time stamps wrong
9411 Deleting slices on moderate sized dataset causes a crash
9439 Context Help for Drift Correction Dialog not working
9501 Crash when deleting Surfaces with contours
9663 Relative size of scale bar font not maintained when scale factor is used
9678 Spots "Voxel count" statistics is zero for some Spots
9749 Hard to determine which license is selected in Administrator
9762 Crash trying to open a second dataset from Arena after adding some manual Filaments
9771 Using context help in some creation wizards fails because of non-existing paths
9788 Imaris is not able to read the time point of .oir file from FV3000 Confocal
9794 Zeiss .lsm file read correctly in 8.3.1 does not load correctly in 8.4.0
9797 Description of 'Maximum Overlapping' tracking algorithm missing
9798 Show Help link for 'Tracking Cells' step broken
9800 Reference Manual states that the Lineage algorithm supports merges
9815 Minimal Y windows size too large
9816 Moving the Reference Frame with color coded objects in scene causes recalculation of statistics on every mouse-over of the rendering area
9819 Aberrant (straight line) path generated by semi-automatic AutoPath
9820 Image from Fiji is disabling "Save as..." in Imaris 8.4
9830 Incorrect visualization of channel intensities in specific file
9846 Wrong time interval in czi file
9851 Surface creation fails on specific 2D data set with 21,400,000 triangles
9852 Context sensitive help link for 3D View Reference Frame Settings does not explain the tab
9853 Annotation is not placed at cursor position
9855 Need new Filament keyboard shortcuts to be documented in the 'Keyboard & Mouse' option under HELP menu
9856 Crash when finishing Creation wizard, if only one of multiple ROI is selected
9865 Crash during start when network drive of file on recent file list not available
9870 'Export statistics' option for a large batched Collection takes a VERY long time to export.
9873 Display of distance transformation channel is failing in surpass and other modes
9887 XT Filament Spine classify has unhindering error message when launched from the .m file
9895 Export of file with manually created tracks causes statistics to re-calculate for a number of hours
9896 Tiled LSM file is read distorted
9899 Opening multi-series TIFF is read improperly in Imaris 8.3 and 8.4
9904 Imaris XT description for tracking surfaces in online Matlab Interface API is not right
9912 Uninstall of Imaris 8.4.x removes IsServerInstalled from the registry
9923 Reference Page For Cell Tracking is too big
9930 Slider in manual Filament tracer in Imaris 8.4 is not linked to cursor
9931 Imaris crash when clicking "File name with Delimiter" in TIFF reader settings
9933 FilamentTracer Undo moves filaments from all time points to the first one
9945 Stripe artifacts after Surface Distance Transformation
9949 Certain Volume settings not saved when using Store
9952 Correct Shortcut description for Filament Autopath in Reference Manual
9958 Rounding issue with Time bar display
9974 flickering brightness of large 3D volume in time lapse
9984 Time wrong for time plot (export) but correct for export all stats or in Vantage
9986 Imaris is not able to read the z voxel size of Olympus .oir file generated from FV3000
10001 Batched Cells data lost when exported to IMS
10002 ND2 timelapse is opening as a single time point
10020 Show help does not work in the Arena Store dialogue
10022 Image of Arena in Preface has bad color resolution
10032 Undo, Redo then Undo again doesn't work anymore
10034 Filaments - Edit Tab - Diameter Field Description in manual to vague
10038 Dataset imported does not get correct Display Adjustment Min/Max settings
10040 Mapped colors are not saved in keyframe animation when IMS with changes to LUT is re-loaded
10048 wrl support not mentioned in reference manual
10061 Image loading in Arena results in 'no mount point found' error message
10071 Track Speed Min and Max inconsistent with respect to Track Speed Mean
10075 Resample images to align reference frames does not do rotational drift in 8.4
10126 Specific file cannot use 1D Vantage plots
10129 Coloc histograms not updated when switching time point
10162 Changing the Coloc ROI Threshold can cause a crash
10192 Update reference manual for Volume Median Intensity statistic
10200 Frame box shadow flickers when voxel size is larger than 1
10208 Mac Arena can't access files on a server requiring domain credentials

Imaris 9.0.1

Fixed 14 Bugs (since Imaris 9.0.0)
10245 Animation 'Frames' textbox loses focus after entry of a single character
10251 Documentation for some Surfaces XT Interface methods missing
10262 Display Adjustments not correctly interpolated in Keyframe Animation
10269 Large jumps along the timebar during Surfaces preview can lead to the preview panel to disappear
10271 Surfaces and filaments statistics documentation needs update and fix
10286 Slow Volume rendering in Imaris 9.0.0
10291 Python XTension XTSurfacesSplit not updated for missing Surfaces functions
10293 Surface model memory usage during detection significantly more in 9.0 than previous versions
10298 Turning off Smoothing in new Surfaces creates huge amount of cache files
10302 Saving stats in Imaris9 does not remember last saved folder location, it changes one up each time
10312 Exported Imaris 9 surface creation parameters re-import with incorrect (grey) icon
10322 Dragonfly licenses (and presumably Imaris core licenses) have the Edit/Draw/Color tabs for Spots and/or Surfaces greyed out
10327 Some .tif images no longer read correctly with Imaris 9
10328 Cutting surface 20-30 cuts results in consistent instability in the cut tool and results in Imaris9 crash

Imaris 9.0.2

Fixed 3 Bugs (since Imaris 9.0.1)
10343 Random crashes in Imaris 9.0 upon edits/updates to the volume data
10290 Navigation Window switches volume rendering to low resolution
10283 Navi viewer no longer shows entire volume, makes navigation difficult