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Imaris 9.2 Release Notes

Welcome to the Imaris 9.2 release notes. Please have a look to the overview of Imaris Release notes for information about prior released features and fixed bugs.

Version Date: June 6, 2018

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

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

GE Incell

Fixed Bugs

Bugs Fixed for Imaris 9.2
10939 Histogram counts more and more tracks when switching between Classify Tracks and Tracking steps
10937 Sholl Radius sorting is wrong in Statistics tab
10900 Creating Imaris9 surface from XT Distance transform channel ignores the pixel intensity that are "0's"
10855 Track Line Width larger than 4 does not display anything on Mac
10853 Crash when deleting filtered dendrites from Filament
10836 Filament Wizard crashes when ROI is used
10821 Filament Statistics Export creates files that cannot be opened in Excel
10820 Cell Distance to Image Border is missing Image information "Img=1"
10809 Surfaces not detected any more when split by seed points is enabled
10803 Using Seed Points for Splitting Surfaces with upper and lower threshold crashes Imaris hard
10766 Background Subtraction "Filter Width" parameter input is ignored
10742 "Import Surface to Cell" only import from the first old surface objects
10741 Cells are missing after clicking on "Finish" in creation wizard
10734 Spots manual placement works only in centre of dataset 1024x1024x1
10725 A certain ims file can not open normally in 3D view
10724 Watershed ignoring surface seed point
10723 Crop 3D window resize does not change image display area
10722 Imaris does not load metadata and datatype of this VSI image correctly
10720 Imaris freezes on Revert when 'Specific channel' is selected in Spots Edit Mode
10706 Spot Manual tracking - 1st time point misplaced
10704 Create Cells on second 2D image crashes Imaris
10689 Coloc tab can become usable in multi-image mode, crashes Imaris
10684 Renamed OME TIFF is not taking the changes to filename upon saving as new OMETIFF
10679 Imaris Stitcher fails on tiles from .CZI image
10677 OME Tiff files from TILL Photonics software crash Imaris
10672 Out Of Memory crash of AutoDepth algorithm
10667 "Frame Rate" option grey out when export movie as "Raw Movie" in Windows
10665 Fit/Reset/Zoom broken for this dataset
10663 File Open dialog creates a nullWindow that interrupts workflow
10651 Hard crash when editing manually created Filaments
10647 Crop3D caused fatal crash in Imaris 9.1
10641 CZI 3D time series volume data not read
10620 Imaris crashes on Delete timepoints if time point range is invalid
10613 Loss of surfaces during import into Cells
10611 Color coding objects based on 2nd image intensities is incorrect when some objects are not in the 2nd image
10607 Imaris crash when deleting 2D Surfaces which is part of a Vantage (Time vs Area)
10594 Center Point Surfaces visualization doesn't offer Subvolume option
10578 Open Image Resampled with slightly larger file causes Imaris to freeze
10577 Contour surface masked generated a false line in the center of masked channel
10564 Imaris wrongly display metadata from ND files generated by Metamorph software
10558 Some vsi files which were previously read as Z=1 now read as Z stacks with a repeating single slice
10533 Imaris is wrongly detecting tiles as timepoints for this slidebook file
10461 Reference Frame statistics after drift correction does not show up
10413 Imaris 9 on OS-X Could not Read .oib file that could previously be read on Imaris 8.4.2
10374 “surface of object" doesn't work on the "Oblique slicer"
10363 Cutting a surface many times can eventually lead to a crash
10351 Batch completes on all files, hitting 100% progress but status remains running with the collection not able to be opened
10295 Distance Transform fails on Surfaces, large 2D dataset
10292 Disable the Size controls in Section view if cross-hair is "off"
9966 saved batched parameters are not reproducing surface results from Arena as seen in Imaris itself
9599 Voxel Calibration of TIFF exported by ImageJ 1.51f (Fiji) not read
9226 Selecting some dozen of items in the "Details" statistics is very slow
9069 Labels do not get removed in statistics list when deleted from objects
7827 3D image with 60,000 or more spots takes long time to load statistics tab
6919 Average Values very slow for large number of time points
6411 Imaris blocked if 'Edit Track' tab active with many single spots
4578 Channel name of duplicated mask channel not displayed

Imaris 9.2.1

Fixed 10 Bugs (since Imaris 9.2.0)
11053 Some images are not recognised as Micromanager any more
11033 Image data inside Leica LIF file is not being handled correctly in Imaris 9.x
11028 Imaris incorrectly converts deconvolved Leica .lif files
10986 Leica .lif file can not be opened in Imaris 9.0 or higher
10954 Imaris stitcher does not read stage coordinates from Deltavision (.dv) files
10898 LIF file open error from mosaic tiling from Leica
10887 Stitcher floating license does not work
10852 Imaris Incorrectly reads certain images in a .lif file
10591 Stage Positions not correctly read for these oif files
10519 CZI FileReader does not correctly handle multi file datasets