Imaris 9.2.0 Release Notes
Welcome to the Imaris 9.2.0 release notes.
Please have a look to the Overview of Imaris Release notes for information about prior released features and fixed bugs.
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Fast rendering for Spots and tracks
With Imaris 9.2 it is possible to interactively render millions of spots. New efficient renderers dramatically improve spot and track rendering speed and make fast rendering possible on normal graphics hardware.
The technology that enables fast spots and tracks rendering is based on the following features
- For each spot only position and radius are uploaded to the GPU
- For each track only segment positions and radius uploaded to the GPU
- Shaders on the GPU compute the rendering
Fast Spots Computation
The computation of spots runs blockwise and multithreaded. It uses system resources efficiently and avoids paging of data to files. It is possible to efficiently compute spots from large 3D images as well as large time series.
Fast Tracking Algorithm
Tracking of many thousands of objects per time point is performed efficiently in Imaris9.2. The linear assignment solver has been improved to speed up the computation of the Brownian Motion, Autoregressive Motion and Lineage tracking algorithms.
Statistics Recalculation Avoided on Spots Editing
When editing spots or tracks statistics will be recalculated only for those objects that require recalculation. For large data this can dramatically improve the time it takes to update statistics.
Multi-Selection on Spots Edit and Surfaces Edit tabs
It is now possible to select multiple spots with a single mouse click. On the spots as well as the surfaces edit tab it is possible to enable three different selection modes: “point”, “circle”, and “box”. “Point” is the normal selection mode where clicks select what is directly under the mouse poniter. In “circle” mode a circle appears around the mouse pointer on the screen and pressing left-click will select all spots whose center lies within the circle. Pressing Ctrl+left-click will add to the existing selection if some unselected spots are within the circle otherwise it will deselect all spots within the circle. The size of the circle on the screen can be changed using the mouse wheel.
Note that when the selected spots are parts of a track the setting from the track editor tab for “Mouse selects” determines how the selection may be expanded for example to select entire tracks.
In box mode a 3D box appears on the screen around the cursor. This box is positioned in 3D and when using left-click or Ctrl+left-click the spots whose center is within the box will be added to or removed from the selection.
Track Editor with Focus and improved usage
To enable working with a large number of tracks the track editor has (turned on by default) a Focus Tracks mode in which only a small number of tracks will be displayed in the trackeditor and the ones that are displayed will be determined based on their proximity to the selected track when “rebuild around selection” is pressed. This allows to focus on tracks that are close to the selected track.
Track Editor “connect”, “disconnect at current time point”, “disconnect all” buttons
In recent previous versions of Imaris connecting and disconnecting a track was surprisingly difficult. In version 9.2 it is possible to efficiently connect and disconnect tracks. The “Connect” button allows to connect selected tracks by extending the first object of a track to a previous object in another selected track. The “Disconnect selected objects at current time point” button breaks the selected tracks at the current time point by deleting connections to objects at previous time points. The “Disconnect all selected objects” button removes all connections (careful with this! If you hit it accidentally, try to immediately hit “connect”).
Statistics Tab large data capable
The statistics tab for objects in Imaris9.2 is capable of handling large numbers of objects interactively.
Labels for Tracks
In Imaris9.2 it is possible to assign label to tracks. Thereby it is possible to get the assigned labels to track statistics and to export them with the statistics.
It is also possible to use “Only show labeled objects” on the color tab to show only those tracks that have labels.
New File Readers
Bugs Fixed for Imaris 9.2
||Histogram counts more and more tracks when switching between Classify Tracks and Tracking steps
||Sholl Radius sorting is wrong in Statistics tab
||Creating Imaris9 surface from XT Distance transform channel ignores the pixel intensity that are "0's"
||Track Line Width larger than 4 does not display anything on Mac
||Crash when deleting filtered dendrites from Filament
||Filament Wizard crashes when ROI is used
||Filament Statistics Export creates files that cannot be opened in Excel
||Cell Distance to Image Border is missing Image information "Img=1"
||Surfaces not detected any more when split by seed points is enabled
||Using Seed Points for Splitting Surfaces with upper and lower threshold crashes Imaris hard
||Background Subtraction "Filter Width" parameter input is ignored
||"Import Surface to Cell" only import from the first old surface objects
||Cells are missing after clicking on "Finish" in creation wizard
||Spots manual placement works only in centre of dataset 1024x1024x1
||A certain ims file can not open normally in 3D view
||Watershed ignoring surface seed point
||Crop 3D window resize does not change image display area
||Imaris does not load metadata and datatype of this VSI image correctly
||Imaris freezes on Revert when 'Specific channel' is selected in Spots Edit Mode
||Spot Manual tracking - 1st time point misplaced
||Create Cells on second 2D image crashes Imaris
||Coloc tab can become usable in multi-image mode, crashes Imaris
||Renamed OME TIFF is not taking the changes to filename upon saving as new OMETIFF
||Imaris Stitcher fails on tiles from .CZI image
||OME Tiff files from TILL Photonics software crash Imaris
||Out Of Memory crash of AutoDepth algorithm
||"Frame Rate" option grey out when export movie as "Raw Movie" in Windows
||Fit/Reset/Zoom broken for this dataset
||File Open dialog creates a nullWindow that interrupts workflow
||Hard crash when editing manually created Filaments
||Crop3D caused fatal crash in Imaris 9.1
||CZI 3D time series volume data not read
||Imaris crashes on Delete timepoints if time point range is invalid
||Loss of surfaces during import into Cells
||Color coding objects based on 2nd image intensities is incorrect when some objects are not in the 2nd image
||Imaris crash when deleting 2D Surfaces which is part of a Vantage (Time vs Area)
||Center Point Surfaces visualization doesn't offer Subvolume option
||Open Image Resampled with slightly larger file causes Imaris to freeze
||Contour surface masked generated a false line in the center of masked channel
||Imaris wrongly display metadata from ND files generated by Metamorph software
||Some vsi files which were previously read as Z=1 now read as Z stacks with a repeating single slice
||Imaris is wrongly detecting tiles as timepoints for this slidebook file
||Reference Frame statistics after drift correction does not show up
||Imaris 9 on OS-X Could not Read .oib file that could previously be read on Imaris 8.4.2
||“surface of object" doesn't work on the "Oblique slicer"
||Cutting a surface many times can eventually lead to a crash
||Batch completes on all files, hitting 100% progress but status remains running with the collection not able to be opened
||Distance Transform fails on Surfaces, large 2D dataset
||Disable the Size controls in Section view if cross-hair is "off"
||saved batched parameters are not reproducing surface results from Arena as seen in Imaris itself
||Voxel Calibration of TIFF exported by ImageJ 1.51f (Fiji) not read
||Selecting some dozen of items in the "Details" statistics is very slow
||Labels do not get removed in statistics list when deleted from objects
||3D image with 60,000 or more spots takes long time to load statistics tab
||Average Values very slow for large number of time points
||Imaris blocked if 'Edit Track' tab active with many single spots
||Channel name of duplicated mask channel not displayed
Bugs Fixed for Imaris Stitcher 9.2
||non-stitched Saved output is corrupted
||Images adjusted with Imaris 9.1 Multiview position parameters (do not display properly in Stitcher 3D view)
||Stitcher Icon on windows installer looks bad