3D

_BinaryCentroids3D, _CleanBinary3D, _CloseBinary3D, _CloseHolesBinary3D, _DilateBinary3D, _DistanceTransformBinary3D, _ErodeBinary3D, _EuclideanCloseBinary3D, _EuclideanDilateBinary3D, _EuclideanErodeBinary3D, _EuclideanOpenBinary3D, _FillHolesBinary3D, _GA3_SpotDetection3D, _GrowObjectsBinary3D, _OpenBinary3D, _SeparateObjectsBinary3D, _SmoothBinary3D, _SpotDetection3D, _SpotDetection3DPrev2D, BinaryCentroids3D, CleanBinary3D, CloseBinary3D, CloseHolesBinary3D, ConvexHull3D, DetectBranching3D, DetectEnding3D, DilateBinary3D, DistanceTransformBinary3D, DistanceTransformBinary3DEx, ErodeBinary3D, EuclideanCloseBinary3D, EuclideanDilateBinary3D, EuclideanErodeBinary3D, EuclideanOpenBinary3D, FillHolesBinary3D, GrowObjectsBinary3D, OpenBinary3D, SeparateObjectsBinary3D, Skeletonize3D, SmoothBinary3D, SpotDetection3D

BinaryCentroids3D

Interactive command to this function: Binary > 3D Processing/Morphology > Create Binary from 3D Centroids

Description 

 BinaryCentroids3D(
   double  Centroid3DSizeUm,
   int  NDDimension
);

Converts the current 3D binary objects to centroids with specified size.

Parameters

double Centroid3DSizeUm

Diameter of the resulting centroids [um]

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

CleanBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Clean

Description 

 CleanBinary3D(
   int  Count,
   int  Kernel,
   int  NDDimension
);

This function performs morphological Clean on a Z-stack of binary layers.

Parameters

int Count

Number of iterations.

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

CloseBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Close

Description 

 CloseBinary3D(
   int  Count,
   int  Kernel,
   int  NDDimension
);

This function transforms current binary image by morphological closing. An interactive equivalent is the _CloseBinary function.

Parameters

int Count

Number of iterations.

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

CloseHolesBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Close Holes

Description 

 CloseHolesBinary3D(
   int  Count,
   int  Kernel,
   int  NDDimension
);

This function removes small holes from current image on a Z-stack of binary layers. An interactive equivalent is the _CloseHolesBinary function.

Parameters

int Count

Number of iterations.

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

ConvexHull3D

This function runs the Binary > 3D Processing/Morphology > Convex Hull command.

Description 

 ConvexHull3D();

DetectBranching3D

This function runs the Binary > 3D Processing/Morphology > Detect Branching on Skeleton command.

Description 

 DetectBranching3D();

DetectEnding3D

This function runs the Binary > 3D Processing/Morphology > Detect Ending on Skeleton command.

Description 

 DetectEnding3D();

Creates 1pixel seeds out of a skeletonized 3D binary image. It preserves only ending points of the skeleton and clears all other pixels.

DilateBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Dilate

Description 

 DilateBinary3D(
   int  Count,
   int  Kernel,
   int  NDDimension
);

The function displays the Dilate on Binary 3D Image dialog box.

Parameters

int Count

Number of iterations.

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

DistanceTransformBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Distance Function

Description 

 DistanceTransformBinary3D(
   int  ResultLocation
);

Parameters

int ResultLocation

Determines how the resulting distance image is shown.

0

A new mono image is created replacing the original color data.

1

New channel with the distance image is created in the current nd2 document.

DistanceTransformBinary3DEx

Description 

 DistanceTransformBinary3DEx(
   int  ResultLocation,
   char *BinLayerNameDst
);

This function performs distance transformation on a Z-stack of binary layers. Please see Binary > 3D Processing/Morphology > Distance Function.

Parameters

int ResultLocation

Determines how the resulting distance image is shown.

0

A new mono image is created replacing the original color data.

1

New channel with the distance image is created in the current nd2 document.

char *BinLayerNameDst

Name of the destination binary layer(s) which will be created by the function.

Note

Some functions accept a list of binary layers. A coma-separated list of names is expected. If the list is in another format than expected or NULL, default names will be used.

ErodeBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Erode

Description 

 ErodeBinary3D(
   int  Count,
   int  Kernel,
   int  NDDimension
);

This function transforms current image on a Z-stack of binary layers by morphological erosions. An interactive equivalent is the _ErodeBinary3D function.

Parameters

int Count

Number of iterations.

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

EuclideanCloseBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Euclidean Close

Description 

 EuclideanCloseBinary3D(
   double  RadiusDouble,
   int  NDDimension
);

This function applies the morphological closing by euclidean sphere on the current 3D binary image.

Parameters

double RadiusDouble

Radius value (µm).

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

See Also

EuclideanDilateBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Euclidean Dilate

Description 

 EuclideanDilateBinary3D(
   double  RadiusDouble,
   int  NDDimension
);

This function applies the dilation by euclidean sphere on a 3D binary image.

Parameters

double RadiusDouble

Radius value (µm).

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

See Also

EuclideanErodeBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Euclidean Erode

Description 

 EuclideanErodeBinary3D(
   double  RadiusDouble,
   int  NDDimension
);

This function applies the morphological erosion by euclidean sphere on a 3D binary image.

Parameters

double RadiusDouble

Radius value (µm).

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

See Also

EuclideanOpenBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Euclidean Open

Description 

 EuclideanOpenBinary3D(
   double  RadiusDouble,
   int  NDDimension
);

This function applies the morphological opening by euclidean sphere on a 3D binary image.

Parameters

double RadiusDouble

Radius value (µm).

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

See Also

FillHolesBinary3D

This function runs the Binary > 3D Processing/Morphology > Fill Holes command.

Description 

 FillHolesBinary3D(
   int  Kernel,
   int  NDDimension
);

Applies the Fill Holes feature to the 3D binary of the current image.

Parameters

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

GrowObjectsBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Grow Objects

Description 

 GrowObjectsBinary3D(
   double  RadiusDouble,
   int  NDDimension
);

Grows the binary layer by the amount specified in the RadiusDouble parameter.

Parameters

double RadiusDouble

Radius value (µm).

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

OpenBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Open

Description 

 OpenBinary3D(
   int  Count,
   int  Kernel,
   int  NDDimension
);

This function transforms current binary image by morphological opening. An interactive equivalent is _OpenBinary function.

Parameters

int Count

Number of iterations.

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

SeparateObjectsBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Separate Objects

Description 

 SeparateObjectsBinary3D(
   int  Count,
   int  Kernel,
   int  NDDimension
);

This function performs morphological Separation of 3D objects on a Z-stack of binary layers.

Parameters

int Count

Number of iterations.

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

Skeletonize3D

This function runs the Binary > 3D Processing/Morphology > Skeletonize command.

Description 

 Skeletonize3D();

Makes a skeleton of the 3D binary image.

See Also 
Skeletonize

SmoothBinary3D

Interactive command to this function: Binary > 3D Processing/Morphology > Smooth

Description 

 SmoothBinary3D(
   int  Count,
   int  Kernel,
   int  NDDimension
);

Performs morphological Smooth on a Z-stack of binary layers.

Parameters

int Count

Number of iterations.

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

SpotDetection3D

Description 

 SpotDetection3D(
   double  EqDiameter,
   double  Contrast,
   int  Kernel,
   int  ProcessComponent,
   int  SpotSize,
   int  Inverted,
   int  CreatePoints,
   int  CreateCircles,
   int  SeparateSpots,
   double  Z-Elongation,
   int  NDDimension
);

Performs 3D spot detection on one color component of the current image.

Parameters

double EqDiameter

Adjusts the size of your object.

double Contrast

Contrast value calculated as a difference between mean intensity inside and mean intensity outside the spot. All the spots with Contrast higher than this value are included into the result.

int Kernel

Shape of the neighborhood defines pixels which will be taken into account.

6

26

int ProcessComponent

Selection of color components.

1

The first component (Blue in RGB image, binary 1)

2

The second component (Green in RGB image, binary 10)

4

The third component (Red in RGB image, binary 100)

7

The first three components (All RGB, binary 111)

Note

The “Brightfield” channel consists of 3 components.

int SpotSize

Spot spinner value.

int Inverted

Color detection method.

0

Bright Spot.

1

Dark Spot.

int CreatePoints

Creates Spots binary.

0

Spots OFF.

1

Spots ON.

int CreateCircles

Creates Circles binary.

0

Circles OFF.

1

Circles ON.

int SeparateSpots

Function separating adjacent 3D spots.

0

Separation OFF.

1

Separation ON.

double Z-Elongation

Elongation in the Z axis.

int NDDimension

Frame selection of the ND document.

0

Current frame

1

Time dimension

2

Multipoint dimension

4

Z dimension

15

All frames (the whole ND document).

16

Selection - the frames/dimensions selected by mouse within the ND control bar will be affected.

Note

Value combination is also possible (e.g.: M+T=3, Z+T=5, M+Z=6).

_BinaryCentroids3D

This function runs the Binary > 3D Processing/Morphology > Create Binary from 3D Centroids command.

Description 

 _BinaryCentroids3D();

Opens the Binary from 3D Object Centroid dialog window enabling to create a new binary layer from centroids.

See Also 
BinaryCentroids3D

_CleanBinary3D

This function runs the Binary > 3D Processing/Morphology > Clean command.

Description 

 _CleanBinary3D();

This function opens the Clean Binary 3D dialog window.

_CloseBinary3D

This function runs the Binary > 3D Processing/Morphology > Close command.

Description 

 _CloseBinary3D();

Opens the Close Binary 3D dialog window.

See Also 
CloseBinary3D

_CloseHolesBinary3D

This function runs the Binary > 3D Processing/Morphology > Close Holes command.

Description 

 _CloseHolesBinary3D();

Opens the Close Holes 3D dialog window.

_DilateBinary3D

This function runs the Binary > 3D Processing/Morphology > Dilate command.

Description 

 _DilateBinary3D();

This function opens a Dilate Binary 3D window.

_DistanceTransformBinary3D

This function runs the Binary > 3D Processing/Morphology > Distance Function command.

Description 

 _DistanceTransformBinary3D();

Opens the Distance Transform 3D dialog window enabling to choose how the resulting distance image is shown.

_ErodeBinary3D

This function runs the Binary > 3D Processing/Morphology > Erode command.

Description 

 _ErodeBinary3D();

Opens the Erode Binary 3D dialog window.

See Also 
ErodeBinary3D

_EuclideanCloseBinary3D

This function runs the Binary > 3D Processing/Morphology > Euclidean Close command.

Description 

 _EuclideanCloseBinary3D();

Opens the Euclidean Close Binary 3D dialog window.

See Also

_EuclideanDilateBinary3D

This function runs the Binary > 3D Processing/Morphology > Euclidean Dilate command.

Description 

 _EuclideanDilateBinary3D();

Opens the Euclidean Dilate Binary 3D dialog window.

See Also

_EuclideanErodeBinary3D

This function runs the Binary > 3D Processing/Morphology > Euclidean Erode command.

Description 

 _EuclideanErodeBinary3D();

Opens the Euclidean Erode Binary 3D dialog window.

See Also

_EuclideanOpenBinary3D

This function runs the Binary > 3D Processing/Morphology > Euclidean Open command.

Description 

 _EuclideanOpenBinary3D();

Opens the Euclidean Open Binary 3D dialog window.

See Also

_FillHolesBinary3D

Description 

 _FillHolesBinary3D();

Applies the Fill Holes feature to the 3D binary of the current image.

See Also 
FillHolesBinary3D

_GA3_SpotDetection3D

Description 

 _GA3_SpotDetection3D(
   int  Inverted
);

Opens the GA3 3D Spot Detection window in the selected color detection mode.

Parameters

int Inverted

Color detection method.

0

Bright Spot.

1

Dark Spot.

_GrowObjectsBinary3D

This function runs the Binary > 3D Processing/Morphology > Grow Objects command.

Description 

 _GrowObjectsBinary3D();

Opens the Grow Objects Binary 3D dialog window used for growing 3D binary objects.

_OpenBinary3D

This function runs the Binary > 3D Processing/Morphology > Open command.

Description 

 _OpenBinary3D();

This function opens the Open Binary 3D window.

See Also 
OpenBinary3D

_SeparateObjectsBinary3D

This function runs the Binary > 3D Processing/Morphology > Separate Objects command.

Description 

 _SeparateObjectsBinary3D();

Executes the 3D binary object separation.

_SpotDetection3D

Description 

 _SpotDetection3D(
   int  Inverted
);

Opens the 3D Spot Detection dialog window.

Parameters

int Inverted

Color detection method.

0

Bright Spot.

1

Dark Spot.

_SpotDetection3DPrev2D

Description 

 _SpotDetection3DPrev2D(
   int  Inverted
);

Opens the Spot Detection dialog window.

Parameters

int Inverted

Color detection method.

0

Bright Spot.

1

Dark Spot.

_SmoothBinary3D

This function runs the Binary > 3D Processing/Morphology > Smooth command.

Description 

 _SmoothBinary3D();

Opens the Smooth Binary 3D dialog window enabling to set the smoothing power on a desired dimension containing the 3D binary.

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