Imaris | Release Notes and Bug Fixes

Imaris 7.6.0 Release Notes

Welcome to the Imaris 7.6.0 release notes. Version Date: October 10, 2012. 
Please have a look to the Overview of Imaris Release notes for information about prior released features and fixed bugs.

[ImarisVantage
[FilamentTracer
[MeasurementPro
[ImarisXT
[Imaris
[Fixed Bugs
[Feedback]
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 ImarisVantage
Boxplots


  • Vantage with Boxplots (Min, Q1, Median, Q3, Max)


    Visualisation of two Surpass Surfaces Objects (red, blue). The plot shows Spericity and 
    Volume over Time. The new Vantage Boxplots appear as projection on the frame border.

  • Boxplots are available with XYZ, Time and Scatter plots. The Box and Whisker Plot, also known as the 5 number summary plot, helps describe a population using easy to interpret visual cues. The 5 numbers it reports are: maximum, third quartile (Q3), median, first quartile (Q1) and the minimum. The top 25% (e.g. biggest) objects will be represented between the Q3 line and the maximum, while the bottom 25% (e.g. smallest) objects will be shown between the Q1 line and the minimum. The remaining 50% of the population will be represented between the Q1 and Q3 lines.

  • In Vantage Time plots the box+whisker representations will be seen in duplicate. Once on the edge of the graph as standard box and line and a second time as a projection plot on the plane related to that parameter (see Time plot examples above)
Creation




  • Multiple Surpass Objects for a single Vantage Plot


    Visualisation of two Surpass Surfaces Objects (red, blue) over time.

    Multiple Objects of the same category (Spots, Surfaces, Cells, Filaments) can be combined in a single vantage plot. This allows to compare the difference of two or more different populations of cells. In order to compare results of different images, we recommend to use the option "Import Scene" from the file menu.

  • The new option "Show Box Plots" in the second step of the creation wizard is activated by default. If you don't want the boxplots, you need to un-check it here.

  • Time-Boxplots appear, if a Time-Plot-Type is selected
Tree


  • After finishing the Vantage creation, multiple Surpass Objects appear as child items of a Vantage.

  • Use the check-box to hide or show the according Surpass Objects in the plot.

  • Select the vantage item to adjust the entire plot, or to adjust properties (e.g. color) of all child items at one. In order to set different properties (e.g. color) for different Surpass Objects, select the Vantage child items.

Edit

  • Secondary and tertiary axis for XYZ


    Different properties (intensities from two channels) of the same Spots

    A secondary (or tertiary) axis can easily be added by pressing the "add" button. This option is useful to compare correlations of properties for the same object. Other example: compare Speed with Volume of Surfaces over Time.

  • Usability improvements: configured plot dimensions are listed including a summary. "Empty" dimensions are no longer disturbing, and new dimensions can be added with the "add" button (x, y, z, color, scale).

  • New checkbox "Show Box Plot" activates the box plot for the selected dimension.

 FilamentTracer
Creation

  • Option to explicitly exclude dark areas

    A) Raw Image B) Filaments 7.5 C) Filaments 7.6

    Images with filamentous structures have often small regions with low intensities. FilamentTracer was developed and optimized to always try to bridge these gaps. This is a disadvantage in case there are small background objects with high intensities (noise - illustration A), because FilamentTracer connects these objects with the main structure (illustration B). With Imaris 7.6 it is possible to explicitly prevent connections in dark image areas (illustration C).

  • Performance of Diameter calculation (Shortest Distance from Distance Map) is improved, and also uses multiple CPU cores. With 4 cores, the calculation is approximately 10 times faster (depends on the image structure).

  • Sholl calculation fixed (pervious Imaris version did count intersections with twisted Dendrites running back towards the Soma not according to the official standard).

MeasurementPro
Measurement Points


  • Angle measurements between three measurement points (polygon mode)



    This is a general tool for measuring angles in 2D/3D space.
Statistics

  • Scientific Notation
  • For all numbers greater than 9999 or smaller than 0.001
    • 12'345 => 1.23e4
    • 0.000'123'45 => 1.23e-4
  • Old Imaris versions display values smaller than "0.001" as "0.000"
  • Settings in menu "Edit / Preferences / Display / Numbers Representation"
    • Unit of Length (m, mm, um, nm)
    • Unit of Time (d, h, min, s, ms, us, ns)
    • Significatn Digits (3..6)

ImarisXT
Interface / XTensions
  • Accelerated Distance Transformation (optimisations + multithreaded). Up to 10 times faster with 4 cores. Hence all the XTensions using this function are much faster.

Imaris
 Spots
  • Faster calculation for "Diameter from Region Border" (multithreaded, approximately 10 times faster with 4 cores)
  • API: Added upper threshold for Surfaces detection
General
  • Support reading of Nikon ND2 V4 Images

Fixed 11 Bugs (since Imaris 7.5.2)
6426 Documentation 7.5.1 Discrepancy between the Estimated XY Diameter Description in Manual and actual behaviour in Imaris 7.5.1
6422 Documentation 7.5.1 Typo in the Reference Manual BoundingBoxOO Description
6405 Documentation 7.5.1 Online documentation link for Tiff Series Reader broken and text outdated
6466 FileIO 7.4.2 Reloading IMS file with cell demo scene crashes Imaris
4030 FileIO 6.4.0 ND2 file reader problem: timelapse with multiple XY positions not opened properly
3093 FileIO 6.1.0 Imaris displays a black image when reading Nikon ND2 file
6538 Slice 7.5.2 Change of Voxel Size not displayed in slice view
5121 Statistics 7.0.0 group statistics reporting improperly for multi-value stats
6407 Surpass Spots 7.5.1 Ellipsoid Object Detection (Z Orientation) hard to find
6533 Vantage 7.5.2 Vantage Time Visualization incorrect when one timepoint has no objects
6354 XT 7.4.2 XT connection and documentation problems

Feedback
Any feedback on the installation, and the usage of Imaris and its features are welcome. Please send your comments to eusupport@bitplane.com

Last Modification: CL, 10-Oct-2012 

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