Click in the middle of an object.
Scroll the mouse wheel. A preview of the future binary layer dynamically appears in the image while you are scrolling the mouse wheel. This defines the approximate size of detected object. Similar objects throughout the image are being detected.
Click the secondary mouse button when you are satisfied with the preview. A binary layer is created.
Smart threshold can be performed repeatedly. The new data are added to the original binary layer.
Create at least two binary layers each representing certain type of scene. E.g.:
Figure 1817. Graph Cut - User Defined Binaries
Run the
Binary > Segmentation > Graph Cut Segmentation command. 
Figure 1818. Graph Cut - Result
Displays/hides all binary layers. Use the O keyboard shortcut.
Synchronizes binary layers with their attached channel.
Creates a new empty binary layer.
Layer3: displayed (checked box) and selected (highlighted) for binary drawing.
Layer2: displayed (checked box), but not selected for binary drawing.
Layer1: hidden (unchecked box), not selected for binary drawing, assigned to the FITC channel.
Select the First Layer and the Second Layer from the combo boxes. Binary operations will be performed between these two layers.
Select the logical operation to be performed. You can also select the Preview check box to view the result of the operation in the image window.
Now choose where the result will appear in the Insert Result into area. You can select to overwrite the data in the first or second layer with the data of the result or to create a new layer containing the result. If so, type the name of the new layer in the edit box.
Click to confirm the action.
Use the
Binary > Skeleton Morphology > Skeletonize command on an existing binary layer. One pixel lines are created.Run
Binary > Skeleton Morphology > Detect Branching on Skeleton to leave pixels just where the line was branching.Use the
Binary > Skeleton Morphology > Skeletonize command on an existing binary layer. One pixel lines are created.Run
Binary > Skeleton Morphology > Detect Branching on Skeleton to leave pixels just on the lines endings.
Binary > Define Threshold 
Note
If you are running NIS-Elements with the Local Option module, the dialog appearance and behavior differs. See below.
Thresholds the image and creates a binary layer. Please see Thresholding.
Figure 1812.
You can create multiple binary layers within one document. Use the View > Analysis Controls > Binary Layers 
control window to manage all binary layers at once.
This button opens a dialog window, which saves the currently thresholded binary as a new layer. Enter Name of the new layer. Set it as visible or not, and specify its color.
Figure 1813.
Apply the command to the whole image sequence, the selected dimension or just the current image frame. See ND2 Files Processing.
(requires: Local Option)
Thresholds the image and creates a binary layer. Please see Thresholding.
Figure 1814.
Pick threshold from image - single pixel, 
, 
Select the picking tool and click on objects in the image you wish to detect. Color values of each of the clicked pixel(s) are used to adjust the low and the high threshold values so that the clicked pixel would stay inside the thresholded interval. To reset the threshold values back to default click 
.
This drop-down menu specifies which channel is thresholded when the Channels mode is selected.
Set to current threshold range
Set to actual (min, max) range
Reset to full rangeThese binary processing functions can be activated and their value adjusted using the arrows or directly by typing the value into the edit box. Fill Holes processing can only be turned on/off whereas the values of other processings are applied as a radius in µm or px.
Filter the detected binary objects using the Size or Circularity restriction filters.
Create New Binary Layer You can create multiple binary layers within one document. Use the View > Analysis Controls > Binary Layers control window to manage all binary layers at once.
Full Image/Use ROI
Save/Load Threshold Settings... Saves/loads the settings of this dialog window to/from a .threshold file.
Open HelpApply the command to the whole image sequence, the selected dimension or just the current image frame. See ND2 Files Processing.
Binary > Threshold Segments color image according to threshold levels for RGB.
This function detects pixels with RGB intensities within the range specified by the Binary > Define Threshold command. Current binary image is the result of the transformation.
See ND2 Files Processing for description of common settings.
Binary > Auto Threshold Performs automatic threshold of the current image.
Figure 1815.
Select one of the available algorithms. Try it on your specimen, to see which one is best for your images:
For more details please see en.wikipedia.org/wiki/Otsu%27s_method.
For more details please see en.wikipedia.org/wiki/Maximally_stable_extremal_regions.
Binary > Smart Threshold This command is designed to threshold objects of similar size and average pixel intensity.
Binary > Spot Detection > Bright Spots This function opens the Spot Detection dialog window in the Bright Spots mode. It is used mainly for detecting circular objects with similar sizes. For more information please see Spot Detection.
Note
General analysis 3 spot detection uses the Different Sizes object detection method.
Binary > Spot Detection > Dark Spots This function opens the Spot Detection dialog window in the Dark Spots mode. It is used mainly for detecting circular objects with similar sizes. For more information please see Spot Detection.
Note
General analysis 3 spot detection uses the Different Sizes object detection method.
Binary > Segmentation > Homogeneous Area Detection Opens the Homogeneous Area Detection dialog window suitable for detecting objects on a homogeneous background and objects which are difficult to segment. Advantage of this function is that the objects do not need to be distinguished by intensity because the function works with edges. This is useful especially for DIC and phase-contrast images.
Figure 1816.
Try which method works best for your image. In some cases, the Variance Based Method may bring better results.
Apply the command to the whole image sequence, the selected dimension or just the current image frame. See ND2 Files Processing.
Binary > Segmentation > Graph Cut Segmentation Implements the so-called “Graph cut algorithm” to enable segmentation of samples where it is impossible to use thresholding or other segmentation methods.
Measurement Sequencer - Definition panel is used for the preparation of advanced measurements which are organized in the Measurement Explorer and executed by the Measurement Sequencer - Run. A set of measurement tools is arranged in five groups enabling to easily define any complex measurement.
Binary > Segmentation > Wound Area Detection This command performs automatic wound detection. It tries to detect homogeneous areas within the image and save the results into a binary layer. It can be well used for analysis of “wound healing” on time-lapse images.
Figure 1819. Dialog on a Z ND2 image
Select a channel to be processed.
On multi-channel images, all channels are processed separately and the resulting binary layers are merged into one.
On RGB images, the intensity component is processed. Intensity = (R+G+B)/3.
Use the Close Holes command to fill holes in the detected objects. Specify how many times the command will be run.
Delete the smallest objects. Specify how many times the command will be run.
Available on non-timelapse images.
This selection enables you to perform logical AND with the previous result (binary layer). Only pixels which were detected in both runs will remain in the binary layer.
Available on timelapse images.
In most cases the Auto threshold function works fine. If you need to adjust your wound area detection threshold more precisely, use the Manual slider.
See ND2 Files Processing.
Binary > Segmentation > Threshold Edges This command finds object edges in the image and marks them by a binary layer.
Figure 1820.
Binary > Segmentation > Segment Tight Borders 
Figure 1821.
Performs the segmentation of binary layer using tight borders detection.
Choose the working channel for the detection (the options depend on the type of the image).
Choose which step will be used in the detection (Threshold Value, Cut Branches, Connect Free Endings, Vanish Objects).
Apply the command to the whole image sequence, the selected dimension or just the current image frame. See ND2 Files Processing.
Binary > Define 3D Threshold (requires: 3D Measurement)
This command thresholds 3D objects. Following window appears:
Figure 1822.
The point is to determine which pixels will and which will not be included in the binary layer and thereby distinguish objects to be analyzed from background. You can define the threshold on an active channel of the image which you can select from the pull down menu. Then move the sliders to define the limit values for selected active channel.
Binary > 3D Spot Detection > Bright Spots (requires: 3D Measurement)
This command detects bright circular objects within a 3D space. Please see Binary > Spot Detection > Bright Spots for further description.
Note
General analysis 3 spot detection uses the Different Sizes object detection method.
Binary > 3D Spot Detection > Dark Spots (requires: 3D Measurement)
This command detects dark circular objects within a 3D space. Please see Binary > Spot Detection > Dark Spots for further description.
Note
General analysis 3 spot detection uses the Different Sizes object detection method.
Binary > Connect 3D Objects in Binaries (requires: 3D Measurement)
Connects Z-stack slices of 2D binary objects into 3D binary objects.
Binary > 3D Processing/Morphology > Open (requires: 3D Measurement)
Performs morphological opening on 3D binary image. See also Binary > Open.
Figure 1823.
Binary > 3D Processing/Morphology > Close (requires: 3D Measurement)
Performs morphological closing on 3D binary image. See also Binary > Close.
Figure 1824.
Binary > 3D Processing/Morphology > Erode (requires: 3D Measurement)
Performs morphological erosion on 3D binary image. See also Binary > Erode.
Figure 1825.
Binary > 3D Processing/Morphology > Dilate (requires: 3D Measurement)
Performs morphological dilation on 3D binary image. See also Binary > Dilate.
Figure 1826.
Binary > 3D Processing/Morphology > Euclidean Open (requires: 3D Measurement)
Figure 1827.
See Also
Binary > Open
Binary > 3D Processing/Morphology > Euclidean Close (requires: 3D Measurement)
Figure 1828.
See Also
Binary > Close
Binary > 3D Processing/Morphology > Euclidean Erode (requires: 3D Measurement)
Figure 1829.
See Also
Binary > Erode
Binary > 3D Processing/Morphology > Euclidean Dilate (requires: 3D Measurement)
Figure 1830.
See Also
Binary > Linear Morphology > Dilate
Binary > 3D Processing/Morphology > Clean (requires: 3D Measurement)
Removes small objects from 3D binary image. See also Binary > Clean 
.
Figure 1831.
Binary > 3D Processing/Morphology > Close Holes (requires: 3D Measurement)
Removes small holes from 3D binary image. See also Binary > Close Holes.
Figure 1832.
Binary > 3D Processing/Morphology > Smooth (requires: 3D Measurement)
Smooths binary image contours in 3D. See also Binary > Smooth.
Figure 1833.
Binary > 3D Processing/Morphology > Separate Objects (requires: 3D Measurement)
Separates 3D binary objects. The lower the Number, the more borders separating the binary objects are introduced.
Figure 1834.
Binary > 3D Processing/Morphology > Fill Holes (requires: 3D Measurement)
Fills holes inside 3D binary objects present in the current volume. Holes touching image borders are not filled.
Binary > 3D Processing/Morphology > Skeletonize (requires: 3D Measurement)
Makes a skeleton of the 3D binary image.
Binary > 3D Processing/Morphology > Detect Branching on Skeleton (requires: 3D Measurement)
Creates 1pixel seeds out of a skeletonized 3D binary image. This function serves for automatic recognition of the intersection points of single-pixel lines.
Binary > 3D Processing/Morphology > Detect Ending on Skeleton (requires: 3D Measurement)
Creates 1pixel seeds out of a skeletonized 3D binary image. It preserves only ending points of the skeleton and clears all other pixels.
Binary > 3D Processing/Morphology > Convex Hull (requires: 3D Measurement)
This function expands non-convex 3D binary image objects to their convex boundaries.
Figure 1835. Example
Binary > 3D Processing/Morphology > Distance Function (requires: 3D Measurement)
This function performs distance transformation on a Z-stack of binary layers. The function calculates distance from the edge of the 3D binary inwards. For uncalibrated documents, pixel distance is used and Z distance is multiplied by 4. For calibrated documents, the distance is calculated in units used for the calibration, then multiplied by 10 and converted into integers. Float distance is not multiplied, µm distance is used instead.
See also Binary > Advanced Morphology > Distance Function and ND2 Files Processing for description of other settings.
Binary > 3D Processing/Morphology > Create Binary from 3D Centroids (requires: 3D Measurement)
This command calculates and marks a centroid on binary image in 3D. Select which method is used to calculate the centroid. See also Binary > Detect > Centroids.
Figure 1836.
Binary > Binary Editor This command opens the binary layer(s) editor. Please see Binary Editor for detailed description of the tools.
Binary > Manual Segmentation (requires: Local Option)
Opens the Manual Segmentation toolbar. Tools for drawing the binaries are red, whereas tools for erasing are blue. Use the Tab button to switch between drawing and erasing. Set the thickness of the drawn elements using the Size drop-down menu or select an existing line thickness (can be different for drawing and erasing). The last chosen tool in drawing/erasing is remembered. Adjust the tools in the 
Settings dialog. Once you start drawing a binary, a new toolbar above the image is shown and a new binary layer is created. You can add a new binary layer by clicking on the 
button. The drawn binaries are saved into the layer which is selected (highlighted). Checking the check box of the specific layer makes the layer visible in the image. The order of the layer buttons can be changed by dragging and dropping them.
If an object or multiple objects are selected, it is possible to click 
on the layer button to move the selected objects into the particular layer.
Each layer can also be attached to an image channel. Simply right-click on the layer rectangle, select Attach To and choose a channel. The attached channel is indicated in the layer button. The button context menu can also be used to detach a layer from a channel (Detach from), remove the selected layer (Remove), rename it (Rename, or use double-click), manually change its color (Change Color), or colorize the objects automatically (Color by Object). Clicking on the colored square of a particular binary layer toggles between the latter two functions.
Figure 1837. Selection of binary layers in manual segmentation.
Tip
Select a channel in the image and then start drawing. A new binary layer is created and it is automatically assigned to the selected channel.
Open View > Analysis Controls > Binary Layers to see an overview of all layers present in the image. Once the binary drawing is finished, click 
Exit Editor or hit .
Undo
Redo
Separate
Fill Holes
Clear Screen Settings Opens the Manual Segmentation - Settings dialog where you can manage custom and predefined presets. Each preset can be adjusted to contain just the tools the user needs (checked items). The order of the tools can be changed by clicking and dragging a tool up/down in the list. Shortcut for each tool or function can be changed by clicking on the shortcut and typing in the new key combination. Once you finish editing your shortcut list, use 
Save or 
Save As... to save it as a preset. Any presets can be selected from the Preset drop-down menu. The selected preset can also be imported (Import 
) or exported ( 
Export) from/to an .msegpreset file. To remove a preset from the preset list, use 
Remove.
A list of other useful shortcuts is shown on the right.
Alternative Polyline and Polygon Drawing - if this option is checked, polylines and polygons are not drawn by straight lines by default but their drawing follows the mouse cursor position without the need of holding down the primary mouse button. To draw straight lines, hold down the primary mouse button. If this option is unchecked, straight lines are drawn by default and the user can hold down the primary mouse button to draw arbitrary shapes.
Tip
When drawing in a zoomed image, hold down Space bar and drag the image to pause the drawing and shift the position of the zoomed image.
Binary > Binary Operations Enables logical transformation of binary images. The Binary Operations dialog box appears.
Figure 1838.
Choose one type of operation using the icons in the top row:
AND (Intersection of Selected Layers)
OR (Union of Selected Layers)
Create Subtraction of the Second Layer from the First Layer Subtraction of the second layer from the first layer will be performed.
Create Subtraction of the First Layer from the Second Layer Subtraction of the first layer from the second layer will be performed.
XOR (Non-equivalence of Selected Layers) Non-Equivalence operation will be performed on the selected binary layers.
EQ (Equivalence of Selected Layers) Equivalence operation will be performed on the selected binary layers.
Copy the first layer First layer will be copied to a layer selected in the Insert Result into option.
Having (Objects from First layer containing any pixel from second one) Takes objects from the first layer based on the condition that they contain at least one pixel from the second layer.
Procedure
Binary > Mask > Define Mask by Threshold Runs the Binary > Define Threshold command and saves the resulting binary layer as the graticule image.
Binary > Mask > Edit Mask Opens the binary editor in which it is possible to draw/edit the graticule mask.
See also Drawing tools
Binary > Mask > Load Mask Displays a dialog window which selects a file with the graticule, previously exported via the Binary > Mask > Save Mask command.
Binary > Mask > Mask Transparency Sets transparency of the graticule mask. The following options are available:
Binary > Mask > Mask Properties Opens the graticule properties window and selects the Mask type. See View > Layers Properties > Graticules Properties. Mask will be activated after clicking the button.
Binary > Open Morphological opening performs Erosion followed by Dilation. This has the effect of clearing all objects which are too small with respect to the specified parameters. Larger structures are not significantly affected.
Figure 1839. Example
The Open on Binary Image dialog box appears.
Figure 1840.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Reset Binary > Close Morphological closing performs Dilation followed by Erosion. It fills all holes in objects which are too small with respect to the specified parameters. Closely neighboring objects get connected.
Figure 1841. Example
Figure 1842.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Binary > Erode Erosion sets each pixel to the value computed as minimum from all pixels in the matrix. Erosion shrinks objects and removes small ones. A non-convex object can split into several parts.
Figure 1843. Example
The following dialog appears.
Figure 1844.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
See Also
Binary > Dilate
Binary > Dilate Dilation sets each pixel to the value computed as maximum from all pixels in the matrix. Dilation expands objects and structures in binary image. Neighboring objects are connected and small holes are filled.
Figure 1845. Example
The following dialog appears.
Figure 1846.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Binary > Erode. Binary > Clean Removes small objects from binary image. This transformation is also called geodesic opening. First, the image is eroded and small objects disappear. Then the remaining eroded objects are reconstructed to their original size and shape. The advantage of this algorithm is that small objects disappear but the rest of the image is not affected. The function can be performed repeatedly.
Figure 1847. Example
Figure 1848.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Binary > Close Holes Removes small holes from the current binary image.
Fills all holes in the binary image which would be destroyed by Erosion of the specified parameters.
Figure 1849. Example
The Close Holes dialog box appears.
Figure 1850.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Binary > Smooth Smooths binary image contours.
Figure 1851. Example
Figure 1852.
It is possible to define the strength of the function by specifying the number of iterations.
Apply the command to the whole image sequence, the selected dimension or just the current image frame. See ND2 Files Processing.
Binary > Convex Hull Expands non-convex binary image objects to their convex boundaries. Convex hull of an object can be defined as the intersection of all half spaces that contain the object, i.e. it is the smallest convex set, which covers the object. This operation uses half spaces rotating in 10 degrees step. Union of all convex hulls is displayed.
Figure 1854. Example
See ND2 Files Processing for description of common settings.
Binary > Detect > Contour This function transforms the binary layer to its contour.
Figure 1855. Example
Binary > Detect > Centroids Converts binary objects to their centroids. Select the method of determining centroid positions.
Figure 1856.
Only the shape of each binary object will be taken into account.
If bright/dark areas dominate aside of the centroid position calculated from just the binary layer, the centroid will be shifted in that direction.
Figure 1857. Example
Binary > Morpho Separate Objects 
Separates binary objects into multiple smaller objects. The higher the Count, the fewer objects will be separated.
Figure 1858. Example
Morpho Separate Objects dialog box appears.
Figure 1859.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Binary > Remove Objects Touching Borders This command deletes every binary object which touches the image border.
Figure 1860. Example
Binary > Linear Morphology > Open Performs morphologic opening on binary image using the selected linear matrix. The choice of the structuring element defines the direction in which the binary image will be affected. See Binary > Open.
Figure 1861. Example
The following dialog appears.
Figure 1862.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Binary > Linear Morphology > Close Performs morphologic closing on binary image using the selected linear matrix. The choice of the structuring element defines the direction in which the binary image will be affected. See Binary > Close.
Figure 1863. Example
The following dialog appears.
Figure 1864.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Binary > Linear Morphology > Erode Performs erosion on binary image, it removes a layer of pixels in the direction of the selected matrix. See Binary > Erode.
Figure 1865. Example
The following dialog appears.
Figure 1866.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Binary > Linear Morphology > Dilate Performs dilation on binary image, it adds a layer of pixels in the direction of the selected matrix.
See also Binary > Dilate.
Figure 1867. Example
The following dialog appears.
Figure 1868.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
See Also
Binary > Erode
Binary > Advanced Morphology > Expand (BinRef=Condition) Performs conditional dilation on binary image.
Note
The current binary image is dilated and then intersected by reference binary image. This step is repeated until there is no difference in the sequence of consecutive images. The current image may be e.g. erosion of the original image copied to reference binary image. In this case the function reconstructs only bigger objects and rejects smaller objects.
See ND2 Files Processing for description of common settings.
Binary > Advanced Morphology > Zones of Influence Creates zones of influence by drawing four connectivity borders. For each pixel of a border between two objects, the distance to both objects is the same.
Figure 1869. Example
Binary > Advanced Morphology > Homotopic Marking Marks objects with homotopic marks. Homotopic marking is a sequential homotopic thinning. It is used for marking objects. A filled object (with no holes) is transformed to a single point. Every hole leaves a closed contour.
Figure 1870. Example
Binary > Advanced Morphology > Pruning Sequentially removes end-points from binary image. This function is used for simplification of skeletons by removal of branches. Closed contours remain unchanged.
Figure 1871. Example
The following window appears.
Figure 1872.
Binary > Advanced Morphology > Hit-Or-Miss Extracts points from binary image according to structuring element. The Hit-Or-Miss Transformation dialog box appears.
Figure 1873.
Note
The Hit-Or-Miss transformation maps binary image to the binary image in the following way: only points that match the structuring element retain in the binary image. Matrix elements values are 0, 1 or 2. 0 specifies the background, 1 specifies the foreground (objects) and 2 specifies that this position in the Matrix can be ignored (either foreground or background). E.g. when selecting Hit-Or-Miss transformation with SinglePoint structuring element, only isolated single points remain in the binary image.
See ND2 Files Processing for description of common settings.
Binary > Advanced Morphology > Thickening Dilates a binary image without changing the number of objects - it is a homotopical transformation.
Figure 1874. Example
When you invoke this command, the Thickening dialog box appears.
Figure 1875.
Binary > Advanced Morphology > Distance Function Displays the distance of each object pixel to the nearest boundary (background pixel) as an intensity value.
The resulting color image is a 16-bit image (to cover distances longer than 255 px)
Figure 1876. Example
The Distance function dialog box appears.
Figure 1877.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
A new channel will be created containing the result of the function (otherwise the current image is converted to a mono image).
Select a binary layer to which the resulting channel will be attached. A virtual link is created, the attached binary layer inherits color of the channel and its visibility is synchronized with the channel. See also View > Analysis Controls > Binary Layers .
Binary > Advanced Morphology > Ultimate Erosion Sequentially erodes binary image, but leaves small areas which would completely disappear in the next erosion.
Figure 1878. Example
The Ultimate Erosion dialog box appears.
Figure 1879.
Click the button to change the structuring element used for this operation. See Structuring Element = Kernel = Matrix.
Binary > Advanced Morphology > Granulometry This command creates the granulometry image from the binary image.
Binary > Advanced Morphology > Fast exoskeleton Creates zones of influence by the fast 'pipe of pixels' algorithm. Performing this command, the ZonesOfInfluenceFast is called and appended to the list of executed functions.
Binary > Advanced Morphology > Medial Axis This command creates medial axis from the current binary objects.
Figure 1880.
Binary > Advanced Morphology > Convert to 4-Connectivity This operation adds pixels to ensure that each pixel which is only 8-connected will become 4-connected. 4-connected pixels are those connected vertically or horizontally, but not diagonally.
See Connectivity.
Binary > Advanced Morphology > Convert to 8-Connectivity This operation removes pixels to ensure that each pixel which is only 4-connected will become 8-connected. 8-connected pixels are those either vertically, horizontally, or diagonally. See Connectivity.
Binary > Advanced Morphology > Connect Objects Connects binary objects which are closer to each other than the specified distance by a thin line.
Figure 1881.
Binary > Skeleton Morphology > Skeletonize Makes a skeleton of the binary image. The current binary image is dilated and then intersected by reference binary image. This step is repeated until there is no difference in the sequence of consecutive images. The current image may be e.g. erosion of the original image copied to reference binary image. In this case the function reconstructs only bigger objects and rejects smaller objects.
Skeleton is a representation that largely preserves extent and connectivity of original binary objects, while pruning most of original pixels.
Figure 1882. Example
Binary > Skeleton Morphology > Detect Branching on Skeleton The purpose of this command is to create 1pixel seeds out of a skeletonized binary image. This function serves for automatic recognition of the intersection points of single-pixel lines.
Figure 1883. Example
Binary > Skeleton Morphology > Detect Ending on Skeleton Purpose of this command is to create 1pixel seeds out of a skeletonized binary image. It preserves only ending points of the skeleton and clears all other pixels.
Binary > Skeleton Morphology > Cut Branches Recursively on Skeleton On a skeletonized binary image, branches (free endings) shorter than the defined length will be removed.
Figure 1884. Example
Figure 1885.
Note
“Recursively” means that the function is called repetitively until there are some branches left to be cut.
Binary > Skeleton Morphology > Connect Free Endings on Skeleton On a skeletonized image, connects branch peaks. Set sensitivity of the function in the window:
Figure 1886.
Binary > Skeleton Morphology > Vanish Objects on Skeleton On a skeletonized image, circular (enclosed) objects with equivalent diameter (eqdia) smaller than the defined value will be deleted. You do not necessarily want to delete small objects but the ones which are mis-detected.
Figure 1887.
Binary > ND Processing > Max Binary Projection (union) This command applies maximum intensity projection to all binary layers of the current T or Z ND2 image (The T or Z dimension is required). The result will be union of the binary layers.
Binary > ND Processing > Min Binary Projection (intersection) This command applies minimum intensity projection to all binary layers of the current T or Z ND2 image. The T or Z dimension is required. The result will be intersection of the binary layers.
Binary > Insert Line, Circle, Ellipse This command can be used for interactive calling of NIS-Elements drawing functions. The Insert dialog box appears.
Figure 1888.
Select the type of geometry you wish to draw (i.e. one of the following):
Calls the InsertLine function which inserts a line in the image.
Calls the InsertLines function which inserts two parallel lines in the image.
Calls the InsertCircle function which inserts a circle in the image.
Calls the InsertEllipse function which inserts an ellipse in the image.
Calls the InsertRectangle function which inserts a rectangle in the image.
Calls the InsertMarkers function which inserts a grid of markers in the image.
Calls the InsertMarker function which inserts one marker.
Number and type of parameters changes accordingly to the selected geometry.
4 or 8, defines the way a line is drawn. See Connectivity.
You can select a logical operation which will be performed between the existing binary layer and the object(s) being inserted.
Closed shapes can be either filled or hollow. Select TRUE to fill the shape or FALSE to leave it hollow.
Depending on the selected geometry, these parameters define distances significant for each shape. Selected Units are used to specify the distances.
When inserting markers, one of the predefined marker shapes can be selected from a pull-down menu.
These parameters specify orientation of the object in degrees [°].
Depending on the selected geometry, these parameters define coordinates significant for placement of the shape (center for a circle, start/end for a line, etc...). Selected Units are used to specify the coordinates.
Select whether the coordinates/dimensions of the shape will be specified in pixels or in the image calibration units.
Note
This option appears only if the current image is calibrated.
See ND2 Files Processing for description of common settings.