Imaris 8.4 Release Notes

Welcome to the Imaris 8.4 release notes. Please have a look to the overview of Imaris Release notes for information about prior released features and fixed bugs.

Version Date: November 10, 2016

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

Fixed Bugs

Imaris 8.4.1