Statistics Generation

Imaris MeasurementPro takes the objects that have been segmented using Imaris’ surface segmentation or spot segmentation methods, refers back to the original data in the identified segmented region, and produces statistical results for each identified object.

• Intensity Statistics Include - Min, Max, Median, Sun, StdDev, and Center on a per channel basis
• Size Statistics Include - Area, Volume, # of Voxels, # of Verticies, and # of Triangles and for spots diameter
• Shape Statistics Include - Ellipsoid Axis Lengths A, B, and C each in the X, Y and Z dimensions, the Ellipticity oblate and prolate, and the Sphericity.
• Positional Statistics Include - Center of Image Mass and Homogeneous Mass in X, Y, and Z
• When combined with ImarisTrack, Imaris MeasurementPro produces track specific statistics outlined in the ImarisTrack features section as well as all the other statistics shown above but for every time point.
• When combined with ImarisCell, Imaris MeasurementPro produces a vast array of cell object-specific statistics outlined in the ImarisCell features section.
• When combined with FilamentTracer, Imaris MeasurementPro produces dendrite and spine specific statistics outline in the FilamentTracer features section.

Interactive Filtering, Sorting, Classifying, Selecting and Grouping Objects based on Statistical Parameters

With the ability to easily generate large amounts of statistical data, it becomes essential for you to easily sort out relevant data and quickly eliminate uninteresting results. Imaris MeasurementPro provides a rich set of functions for quick, interactive selection.

• Filtering – Both during the creation process for "Surface Objects", "Spot Objects", "Cells" or "Filaments" and once again after the objects have been created, Imaris MeasurementPro allows you to include or exclude objects based on any calculated statistical parameter. (Imaris Cell and Filament Tracer are needed to use Cells and Filaments)

1. Choose any statistical parameter from a drop down menu
2. Select in a histogram or type in values to include or exclude
3. Objects meeting the selection criteria are automatically and interactively shown in real time in the 3D/4D view.
4. Combinations of statistical parameters may be used to filter on multiple criteria
5. Guesswork is eliminated

New similarity filters - This function lets the user to identify the potential similarity among other objects within the image. Select reference object and its statistics, obtain a difference between this object and the remaining ones, sort them according to pre-selected statistics to highlight similarities. This function is an XTension and requires ImarisXT.

• Sorting And Classifying – The statistics tab in Imaris MeasurementPro allows the data to be sorted based on any statistical parameter. You can select one or many objects from the list and they are automatically selected in the visual view.
• Selection – In addition to selecting objects via filtering, sorting, or classifying them, you may pick single or combinations of objects from the visual view by simply clicking on then. The associated statistics are highlighted in Imaris.
• Grouping – Any object that has been selected via one of the methods above may be copied to a new group. The original segmentation is retained for future use and the new group may be colored independently of the rest of the objects or have its statistics exported separately.

Statistical Output

Imaris MeasurementPro presents a Statistics Tab to conveniently work with statistical values for further analysis.

• Export - Easily export statistical values as .csv, Excel .xml or native Excel .xls files. Exported statistical values are compatible with open-office and suitable for MAC users.
• Timeplot – Time dependant specific values can be displayed via graphical representation. You can select a time point of interest in the graph and the visual view in surpass changes accordingly (requires ImarisTrack).
• Averages - For images that contain multiple objects, the average of each statistical parameter for all objects in the image is calculated. These averages are calculated for spots objects, surface objects, and filament objects.
• Color Coded Values – Choose a statistical parameter and color code your statistical values based on this statistic for visual clarity.
• Find Objects – Search for objects by ID number, or click on your object to obtain the corresponding ID number. If you're doing the statistical analysis outside of Imaris (e.g. Excel), you still can find the objects by ID number. From the ID number identified with the statistic in excel, enter it into the search function in Imaris and the object is automatically selected in the visual view.

Interactive 3D Angle, Distance and Intensity Measurements

Imaris MeasurementPro allows you to interactively place points anywhere in 3D space and quickly measure angles, distances and intensities between them.

• Position – Measurement points can be placed to any position in the 3D volume image using the “AutoDepth” algorithm for automatic 3D positioning. Measurement points can be placed on any “Surpass” component such as an “Ortho Slice”, “Oblique Slice”, and on “Spots”, “Surfaces”, or “Filaments”, "Cells" or measurement points can be positioned via numerical input. Measurement points can also be used to measure distances between non-segmented volume rendered data. The 3D cursor interacts preferentially with (a) the most intense voxels of all channels, (b) the most intense voxels of a specific channel or (c) solid segmented objects such as Surfaces.
• Customize – Customize the display by choosing different point shapes, colors and adjustable font sizes. Choose to measure between two points at a time or an entire series of points.
• Line Intensity Profiles – Along any line that is measured a line intensity profile can be created in Imaris MeasurementPro.

Contour Surface Generation

Imaris MeasurementPro provides a powerful tool to semi automatically draw user-defined surfaces across slices of a z-stack. These semi automatic or “Contour Surfaces” can be used to obtain statistical measurements like any other “Surface Object” but only for the area drawn. "Contour Surfaces" can be used if threshold based surfaces segmentation fails (electron microscopy, silver stain), or to create ROIs for ImarisColoc or to be used as a mask.

• Build Objects – Generate smooth, accurate objects, which offer maximum image quality and high volume precision from 2D contours.
• Draw Contour Surfaces – Draw contours by clicking into individual 2D planes in the image. Zoom or pan as needed; pause or resume contour drawing at any time. Click to add or delete points that define the contour of the object so that the most precise description of the object of interest can be obtained. Build sophisticated objects that fork or merge on section planes.
• Trace Contour Surfaces – Trace contours while the system automatically inserts vertices at user-defined intervals – either lapsed time or distance. In addition, the isoline and the magic wand tools can automatically detect complete 2D contours (automatic edge detection). Finally, the "auto adjust" tool can automatically refine the manual, semi-automatic or automatic detection of 2D contours.
• Flexibility – Combine manually built with automatically generated objects such as surfaces or any other surpass object.

General

• Requires Imaris
• Provides statistical data for the original image and for objects segmented with Surfaces, Spots, Contour Surfaces, Cells* or Filaments*.
• Provides statistics data for tracks, "Cells" and "Filaments" only in combination with Imaris Track, Imaris Cell and Filament Tracer, respectively.
• Provides interactive selection, sorting, filtering, classification, and grouping of objects
• Provides statistical output
• Provides interactive 3D angle, distance and intensity measurements as well as line profiles
• Provides for Contour Surface (Manual surface) generation
• Imaris uses Standard Scientific Notation throughout

* Imaris Cell and Filament Tracer needed

Statistics Generation

• Enables the Statistics Tab to be displayed
• Overview Statistics Tab – Gives a summary of total values of all sub objects measured
• Detailed Statistics Tab – Displays the statistics of all objects at the selected time point
• Specific Values - Allows the user to select any one measured statistical parameter
• The list is specific to all the objects at one time point. It changes as the user changes time points
• The list can be sorted
• When used with Imaris Track and a specific track or tracks are selected, a graph showing the change in the selected statistical parameter over time is displayed
• Provides interactive selection, sorting, filtering, classification, and grouping of objects
• Provides statistical output
• Provides interactive 3D angle, distance and intensity measurements as well as line profiles
• Provides for Contour Surface (Manual surface) generation
• Imaris uses Standard Scientific Notation throughout
• Average Values - For images that contain multiple objects, the average of each statistical parameter for all objects in the image is calculated
• The list shows the min, max, mean, Std dev, Median, sum, and count for each value
• The list is specific to all the objects at one time point. It changes as the user changes time points
• All Values – All statistical values calculated for all objects at the current time point
• Selection Statistics Tab - Displays statistics only for the selected object(s)
• Specific Values - Allows the user to select any one measured statistical parameter
• A list showing only the selected objects with the selected statistical parameter.
• The list is specific to all the objects at one time point. It changes as the user changes time points
• The list can be sorted
• Average Values
• The list shows the min, max, mean, Std dev, Median, sum, and count only for the selected objects
• The list is specific to all the selected objects at one time point. It changes as the user changes time points
• All Values – All statistical values calculated for the selected objects at the current time point
• Statistical parameters to be displayed can be activated or deactivated based on users needs
• All statistics are automatically calculated on a per time point basis for 4D data
• Volume Object Statistics
• Number of Voxels, Data Volume
• Intensity: Sum, Mean, and Standard Deviation per channel
• Surface Object Statistics (Any Surface Object – Manual, Automatic, Semi-Automatic)
• Overall Values (Group Totals)
• # of Voxels, # of Triangles, # of Surfaces, # of Surface per time point
• Size ( Each individual object)
• # of Voxels, # of Triangles, # of Vertices
• Area, Volume
• Shape (Each individual object)
• Ellipsoid Axis Lengths A, B, and C each in the X, Y, and Z dimensions
• Ellipticity obate and prolate
• Sphericity
• Position
• Center of Image Mass and Homogeneous Mass in X,Y, and Z
• Time Index
• Intensity - Min, Max, Median, Sun, StdDev, and Center on a per channel basis
• Spot Object Statistics
• Overall Values (Group Totals)
• - # of Spots, # of Spots per time point
• Size ( Each individual object)
• # of Voxels
• Area, Volume
• Diameter
• Position
• Center X, Y, and Z
• Time Index
• Intensity - Min, Max, Median, Sun, StdDev, and Center on a per channel basis
• Track Statistics – Requires both ImarisTrack and Imaris MeasurementPro. See ImarisTrack for details
• Cell Statistics - See ImarisCell for details
• Filament Statistics - See FilamentTracer for details

Selection, Filtering, Grouping, Classification

• Selection
• Pick any single or combination of objects from the visual view by clicking on them – the associated statistics are selected in the statistics tab
• Pick any single or combination of object statistics in the statistics tab and the associated objects are selected in the visual view
• Selection is completely interactive and real-time
• Filtering
• Choose any statistical parameter from a drop down menu
• Select in a histogram or type in values to include or exclude
• Objects meeting the selection criteria are automatically and interactively shown in real time in the visualization of the image.
• Combinations of statistical parameters may be used to filter on multiple criteria
• Similarity filter - an XTension for finding similarity of objects in relation to pre-selected statistics of a reference object. Requires ImarisXT
• Duplicate filtered or selected objects to an new main object to group them
• Grouped objects can have global properties applied to them such as color and transparency
• Statistical output can be exported only from a single group – See Statistics Output
• Classify objects by using multiple filters or selection methods
• Highlight objects with varying statistics by color-coding their appearance based on any statistical parameter calculated

Measurement Points: 3D Angles, Distance, Intensities and Line Profiles

• Creation of Measurement Points
• Can be placed in the volume image
• Can be placed on orthogonal or oblique slices
• Can be place on Spots, Surfaces, Filaments and Cells.
• Placement is made interactively using the AutoDepth function while clicking in the visual image
• Points have an X, Y, Z and time position
• Points may be altered manually (shifted or moved)
• Visualization
• Measurement Points
• Displayed as open or closed Spheres, Cubes, or Tetrahedrons
• Diameter and color of the points can be altered
• Display label and intensity values as required
• Change font and color of labels
• Measurement Line
• Measure Pairs (A-B, C-D, etc) or Polygon (A-B-C-D, …)
• Change line width
• Add line distance labels
• Add intensity measurement labels at each point
• Add angle measurement labels between three points (polygon option)
• Multiple measurement point objects with different settings may be added to the Surpass scene
• Statistics
• Overall – Number of points placed
• Detailed
• Angle between three points (polygon mode) - Distance between each pair
• Total distance
• Intensity at the center of each measurement point on a per channel basis
• Position of the measurement point in X, Y, Z, and t
• Line Profile
• A plot of the intensity along each measurement line in 3D space
• Completed on a per channel basis
• Any or all measurement pairs may be selected
• Graph may be exported

Contour Surfaces

• Uses
• To manually and semi-automatically segment regions where other methods fail
• To create arbitrarily shaped ROI’s
• To use as a mask to exclude or include data
• Creation
• Draw on a series of 2D slices to create a 3D object
• Drawing outlines the manual region of interest. Additionally, the "isoline" or "magic wand" tools can be used to automatically detect complete 2D contours (automatic edge detection).
• Drawing slice can be positioned in the XY, XZ, or YZ planes
• Drawing can be completed by clicking into the image for every anchor point
• Anchor points can be placed automatically every X second or after X distance for more automated drawing
• Anchor points can be added, removed, or moved after drawing to get the prefect outline of the object or region being traced
• Draw only on slices where changes in shape occur, the software will interpolate between the slices that have been drawn on
• Copy the drawing from one slice to another and then adjust the drawing to save time
• Result
• A surface object is the result of an manually drawn contour surface
• The surface behaves like any other Imaris surface object

Statistics Output

• Generate output files as Comma Separate Value (CSV), Excel (.xml or .xls)
• Output files are compatible with Open Office and Macintosh
• Output only the statistics in the selected tab (Overview, detailed, or selection)
• Output all statistics calculated
• Object ID #’s
• Each object has a unique ID # to identify it
• Object ID’s are shown in the statistics tab and in the output file
• Enter the ID number in the search field and search. The object is then highlighted (selected) in both the statistics list and the visual view