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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
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
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.
Performance tests show that Imaris9 computes surfaces almost an order of magnitude faster than Imaris8.4.1.
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.
Imaris9 is the first Imaris version that natively renders 2D surfaces as 2D. (Previous versions of Imaris computed 3D surfaces from 2D images.)
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.
The Transfer Function settings are stored in the IMS file separately from the display min/max.
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.
Imaris9 has an auto adjust functionality that is available on the volume settings tab in normal shading mode.
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.
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.
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.
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.
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)
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).
System preferences are automatically migrated during installation of Imaris. User preferences are automatically migrated on first start of Imaris.
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).
| 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 |
| 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 |
| 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 |
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