9 List of Workflow Modules

Each section below describes one workflow module. The section name consists of the name of a module as it is presented in the C window of the bambu GUI and the full name of operation. The contents of the section presents the short explanation of how this module works. For detailed explanation and general information on image processing consult [2]. The number and type of input and output ports are listed under input and output entries, respectively. The parameters that can be adjusted for this operation are listed under parameters entry.

9.1 align - Generate rules to correct the embryo orientation

This operator generates the rules to put the image of Drosophila embryo into standard orientation. It checks whether the posterior part of an embryo is larger than the anterior one, and whether the ventral part is larger than the dorsal one. The output text file contains the list of needed operations.

input
1 image:.tif
output
1 text:.txt

The format of an output file:

<alighn>
transpose or - if not needed
reversecolumn or - if not needed
reverserows or - if not needed
</alighn>

9.2 andif - Anisotropic diffusion

Diffusion algorithms remove noise from an image by modifying the image via a partial differential equation (PDE). Anisotropic diffusion lets the diffusion coefficient to vary spatially so as to enhance the intra-region smoothing in preference to the inter-region one. Region boundaries remain sharp. The details can be found in [4]. The PDE is discretized in space using the pixel locations as knots of the grid. The original image is used as the initial condition and the PDE is numerically integrated over time with the integration ("time") step and the number of iterations supplied as parameters. Two edge-stopping functions were proposed in the original paper. The additional parameter called Threshold controls the "sensitivity" of the edge-stopping function. The parameters are to be determined experimentally to achieve the desired result.

input
1 image:.tif
output
1 image:.tif
parameters
Number of iterations
Time step(<=1)
Threshold(<1) for edge stopping function
The type of edge stopping function

9.3 apee - Correct orientation of embryo

This operator applies the rules to put the image of Drosophila embryo into standard orientation. These rules are generated by the align (see 9.1) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif

9.4 apro - Filter the table

This operator filters the input table of numerical values. The table can consist of an arbitrary number of rows greater than one. The number of columns should be greater than two. The output consists of two columns. Parameters X and F define the numbers of columns in input table that are printed in the output. The rows are selected by the following rule: Y min < Y < Y max, where Y represents the value of the current row in the third column of the input table. The rows of the output are sorted with respect to the first column. Consequently, the output can be directly fed to the gnuplot.

input
1 text:.txt
output
1 text:.txt
parameters
X – number of the column for the argument,
F – number of the column for the function value,
Y min – lower bound for y,
Y max – upper bound for y.

9.5 apron - Filter the data

This operator filters the input table of numerical values. The table can consist of an arbitrary number of rows greater than one. The number of columns should be greater than two. The output table consists of all columns from the input. The rows are selected by the following rule: Y min < Y < Y max, where Y represents the value of the current row in the third column of the input table. The rows of the output are sorted with respect to the second column. Consequently, the output can be directly fed to the gnuplot.

input
1 text:.txt
output
1 text:.txt
parameters
Y min – lower bound for y,
Y max – upper bound for y.

9.6 apsc - Check the orientation of embryo

This operator checks the rules generated by align (see 9.1) operator using the result of chemar (see 9.18) operator. The resultant rules can be used to correct the orientation.

input
1 text:.txt
2 text:.txt
output
1 text:.txt
parameters
Direction – indicates in which part of an embryo ( A(anterior) or P(posterior)) the level of gene expression should be higher.

9.7 ar_minus - Subtract the image dimensions

This operator subtracts the image dimensions that are given as a string of four numbers which are distances measured in pixels from the image center to its borders. These dimensions can be calculated by the halfsizes (see 9.62) operator.

input
1 text:.txt
2 text:.txt
output
1 text:.txt

9.8 ar_plus - Sum up the image dimensions

This operator sums up the image dimensions that are given by a string of four numbers which are the distances measured in pixels from the image center to its borders. The dimensions can be calculated by the halfsizes (see 9.62) operator.

input
1 text:.txt
2 text:.txt
output
1 text:.txt

9.9 ar_x - Multiply the image dimensions by a constant

This operator multiplies by a constant the image dimensions given by a string of four numbers which are the distances measured in pixels from the image center to its borders. The dimensions can be calculated by the halfsizes (see 9.62) operator. The constant is defined as a parameter.

input
1 text:.txt
output
1 text:.txt
parameters
Value – the multiplier.

9.10 arcplot - Average the intensities over bins

This operator averages the intensities over bins defined in polar coordinates. The input file must contain the list of pixels in polar coordinates. The output contains the table of bins with average angle (theta) and the value of average intensity in a bin.

input
1 text:.txt
output
1 text:.txt
parameters
Rho – lower bound for radius,
Rho max – upper bound for radius,
Rho bins – number of bins along the radius,
Theta min – lower bound for theta,
Theta max – upper bound for theta,
Theta bins – number of bins along the arc.

9.11 avg - Average images pixel by pixel

This operator averages three images pixel by pixel.

input
1 image:.tif
2 image:.tif
3 image:.tif
output
1 image:.tif

9.12 avg2 - Average images pixel by pixel

This operator averages two images pixel by pixel.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.13 blo2pol - Convert the coordinates to polar coordinates

This operator converts the coordinates of centroids of blobs to polar coordinates. The center of coordinate system is calculated from the input mask image. The list of blobs is input to the second port and can be calculated by the blob (see 9.14) operator.

input
1 image:.tif - mask image
2 text:.txt
output
1 text:.txt

9.14 blob - Extract the objects from the binary image

Contiguous regions of "on" pixels surrounded by "off" pixels (blobs) are stored in the output as the list of pixel indices. The limits are checked for the number of pixels in the region. The number of blobs is also limited. If the input images are different the first is treated as the image of domains each of which contains not more than one blob. The list of pixel indices for the domains containing blobs is also stored in the output. This makes it possible to attach the information of the surroundings to the blobs.

input
1 image:.tif
2 text:.txt
output
1 text:.txt
parameters
Minimal number of pixels
Maximal number of pixels
Maximal number of blobs

9.15 bolb - Draw an image of the blobs

This operator restores an image of blobs from the list stored in the input file.

input
1 text:.txt
output
1 image:.tif

9.16 bolin - Draw an image of the selected blob

This operator restores an image of the selected blob from the list stored in the input file. The blob is selected by the index.

input
1 text:.txt
output
1 image:.tif
parameters
Index – index of the blob.

9.17 canny - Canny Edge detector

This operator implements the Canny algorithm for edge detection.

input
1 image:.tif
output
1 image:.tif
parameters
Low threshold - the minimal value of gradient magnitude,
High threshold - the maximal minimal value of gradient magnitude,
Aperture size - size of window to calculate the magnitude of gradient

9.18 chemar - Check the orientation of the Drosophila embryo

This operator calculates the average intensity in the left and right parts of the image.

input
1 image:.tif
output
1 text:.txt

Format of the output file:
<chemar>
R - if the the average intensity on the left is greater and L otherwise,
"average intensity on the left" "average intensity on the right",
</chemar>

9.19 chole - Closing of holes

This operator fills the regions of "off" pixels surrounded by "on" pixels using a structural element. Unclosed contours are erased. The structural element can be calculated by the strel (see 9.141) operator.

input
1 image:.tif
2 text:.txt - structural element
output
1 image:.tif

9.20 chole3d - Closing of holes

This operator fills the regions of "off" pixels surrounded by "on" pixels using a structural element. Unclosed contours are erased. The structural element can be calculated by the strel3d (see 9.142) operator.

input
1 image:.tif
2 text:.txt - structural element
output
1 image:.tif

9.21 cmove - Move data using curl

This operator moves data between servers using curl utility.

input
1 image:.tif
output
1 image:.tif
parameters
Scheme – http or https.
Uri – address.
Login – username.
Pasword – password.

9.22 cmove_i - Move data using curl

This operator moves data between servers using curl utility.

output
1 image:.tif
parameters
Scheme – http or https.
Uri – address.
Login – username.
Pasword – password.
Image – file name.

9.23 crop - Crop image

This operator reduces the dimensions of the input image to the minimal rectangular area required to cover all "on" pixels. The number of erased pixels is stored in the second output file that can be used to crop other images by the geometry (see 9.51) operator.

input
1 image:.tif
output
1 image:.tif
2 text:.txt

The format of output file:
<crop>
upper offset,lower offset, left offset, right offset - numbers of pixels cropped at each side,
</crop>

9.24 curlup - Move data using curl

This operator moves data between servers using curl utility.

input
1 image:.tif
parameters
Scheme – http or https.
Uri – address.
Name – file name.
Login – username.
Pasword – password.

9.25 cwtsd - Watershed transform

This operator makes a watershed transformation of an input image. The connectivity can be defined as a parameter.

input
1 image:.tif
output
1 image:.tif
parameters
Connectivity - defines the neighborhood: 4 or 8.

9.26 cwtsd3d - Watershed transform

This operator makes a watershed transformation of an input image. The connectivity can be defined as a parameter.

input
1 image:.tif
output
1 image:.tif
parameters
Connectivity - defines the neighborhood: 6 or 26.

9.27 decbsup - Blind deconvolution

This operator performs a blind deconvolution of the input image. It reads the initial guess for the PSF parameters from the second input. It also prints the PSF approximation in the second output.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
2 text:.txt
parameters
Max.num.of iterations - maximal number of iterations.
Max.blind iter - maximal number of iterations for each PSF guess.
Criterion - stopping criterion.
Lambda - Laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.

9.28 decbsup_i - Blind deconvolution

This operator performs a blind deconvolution of the input image. The initial guess for the PSF parameters is provided as the parameters. It also prints the PSF approximation in the second output.

input
1 image:.tif
output
1 image:.tif
2 text:.txt
parameters
Max.num.of iterations - maximal number of iterations.
Max.blind iter - maximal number of iterations for each PSF guess.
Criterion - stopping criterion.
Lambda - Laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.
PSF parameter - standard deviation.
Window - -1 for auto.

9.29 decinv - Inverse filter

This operator performs deconvolution of the input image using inverse filter. It reads the initial guess for the PSF parameters from the second input.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Lambda - Laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.
Gamma - regularization coefficient.

9.30 decinv_i - Inverse filter

This operator performs deconvolution of the input image using inverse filter. The initial guess for the PSF parameters is provided as the parameters.

input
1 image:.tif
output
1 image:.tif
parameters
Lambda - Laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.
Gamma - regularization coefficient.
PSF parameter - standard deviation.
Window - -1 for auto.

9.31 decsup - Richardson-Lucy deconvolution

This operator performs deconvolution of the input image using Richardson-Lucy algorithm. It reads the initial guess for the PSF parameters from the second input.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Max.num.of iterations - maximal number of iterations.
Criterion - stopping criterion.
Lambda - laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.

9.32 decsup_i - Richardson-Lucy deconvolution

This operator performs deconvolution of the input image using Richardson-Lucy algorithm. The initial guess for the PSF parameters is provided as the parameters.

input
1 image:.tif
output
1 image:.tif
parameters
Max.num.of iterations - maximal number of iterations.
Criterion - stopping criterion.
Lambda - laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.
PSF parameter - standard deviation.
Window - -1 for auto.

9.33 dectm - Tikhonov-Miller deconvolution

This operator performs deconvolution of the input image using Tikhonov-Miller algorithm. It reads the initial guess for the PSF parameters from the second input.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Lambda - laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.
Gamma - regularization coefficient.

9.34 dectm_i - Tikhonov-Miller deconvolution

This operator performs deconvolution of the input image using Tikhonov-Miller algorithm. The initial guess for the PSF parameters is provided as the parameters.

input
1 image:.tif
output
1 image:.tif
parameters
Lambda - laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.
Gamma - regularization coefficient.
PSF parameter - standard deviation.
Window - -1 for auto.

9.35 decwiener - Wiener filter

This operator performs deconvolution of the input image using Wiener filter. It reads the initial guess for the PSF parameters from the second input.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Lambda - laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.
Gamma - regularization coefficient.
Alpha - Value 1 corresponds to the classic Wiener filter.

9.36 decwiener_i - Wiener filter

This operator performs deconvolution of the input image using Wiener filter. The initial guess for the PSF parameters is provided as the parameters.

input
1 image:.tif
output
1 image:.tif
parameters
Lambda - laplace coefficient.
PSF type - bessel,gauss,exp,ones or confocal_beessel.
Gamma - regularization coefficient.
Alpha - Value 1 corresponds to the classic Wiener filter.
PSF parameter - standard deviation.
Window - -1 for auto.

9.37 despekle - Reduce speckle noise in the input image

This operator reduces the intensity of salt and pepper noise in an image using the Crimmins complementary hulling algorithm [1]. This algorithm smoothes the image by reducing the magnitude of locally inconsistent pixels, as well as by increasing the magnitude of pixels in the neighbourhood surrounding a spike. The spike is defined here as a pixel whose value is different from its surroundings by more than 2 intensity levels. Increasing number of iterations of the algorithm can introduce an effect of blurring of the image. In the ultimate case all sharp gradients will be smoothed down to a magnitude of 2 intensity levels. case

input
1 image:.tif
output
1 image:.tif
parameters
Iterations - number of sweeps.

9.38 despekle3d - Reduce speckle noise in the input image

This operator reduces the intensity of salt and pepper noise in an image using the Crimmins complementary hulling algorithm [1]. This algorithm smoothes the image by reducing the magnitude of locally inconsistent pixels, as well as by increasing the magnitude of pixels in the neighbourhood surrounding a spike. The spike is defined here as a pixel whose value is different from its surroundings by more than 2 intensity levels. Increasing number of iterations of the algorithm can introduce an effect of blurring of the image. In the ultimate case all sharp gradients will be smoothed down to a magnitude of 2 intensity levels. case

input
1 image:.tif
output
1 image:.tif
parameters
Iterations - number of sweeps.

9.39 diglsm - Distance transform

This operator extracts one channel from the multichannel LSM image.

input
1 image:.tif
output
1 image:.tif
parameters
Channel - the channel to extract.

9.40 distance - Distance transform

This operator replaces the value of each pixel in the input image by the Euclidean distance from this pixel to the nearest "off" pixel. The Window parameter defines the size (in pixels) of the neighbourhood of the pixel under consideration used in calculations.

input
1 image:.tif
output
1 image:.tif
parameters
Window- defines the approximation of the distance measure.

9.41 distance3d - Distance transform

This operator replaces the value of each pixel in the input image by the Euclidean distance from this pixel to the nearest "off" pixel. The Window parameter defines the size (in pixels) of the neighbourhood of the pixel under consideration used in calculations.

input
1 image:.tif
output
1 image:.tif
parameters
Window- defines the approximation of the distance measure.

9.42 edge - Edge detection

This operator detects the edges of objects in the input image using the Shen-Castan Detector [5, 6].

input
1 image:.tif
output
1 image:.tif
parameters
a1, a2 - parameters of the Infinite Symmetric Exponential Filter (ISEF), 0 < a1 < 1, 0 < a2 < 1.
Low threshold - the minimal value of gradient magnitude,
High threshold - the maximal minimal value of gradient magnitude,
Window - size of window to calculate the magnitude of gradient,
Segment - minimal number of pixels in the edge segment. The width or height of a window cannot be an even number,
Connectivity - 4 or 8-neighborhood

9.43 edge3d - Edge detection

This operator detects the edges of objects in the input image using the Shen-Castan Detector [5, 6].

input
1 image:.tif
output
1 image:.tif
parameters
a1, a2 - parameters of the Infinite Symmetric Exponential Filter (ISEF), 0 < a1 < 1, 0 < a2 < 1.
Low threshold - the minimal value of gradient magnitude,
High threshold - the maximal minimal value of gradient magnitude,
Window - size of window to calculate the magnitude of gradient,
Segment - minimal number of pixels in the edge segment. The width or height of a window cannot be an even number,
Connectivity - 6 or 26-neighborhood

9.44 expand - Expand image via pixel replication

This operator increases the size of the input image using the pixel replication.

input
1 image:.tif
output
1 image:.tif
parameters
Scale - the scale factor.

9.45 expand3d - Expand image via pixel replication

This operator increases the size of the input image using the pixel replication.

input
1 image:.tif
output
1 image:.tif
parameters
Scale - the scale factor.

9.46 fill - Fill the holes

This operator fills the regions of "off" pixels surrounded by "on" pixels.

input
1 image:.tif
output
1 image:.tif
parameters
Connectivity - 4 or 8 neighbourhood.

9.47 gclose - Morphological closing

This operator performs morphological closing which is the dilation followed by erosion using the structural element supplied as the second input. The structural element can be calculated by the strel (see 9.141) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions - number of sweeps.

9.48 gclose3d - Morphological closing

This operator performs morphological closing which is the dilation followed by erosion using the structural element supplied as the second input. The structural element can be calculated by the strel3d (see 9.142) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions - number of sweeps.

9.49 gdilation - Dilation

This operator does successive dilations of the input image by the structural element supplied as the second input. The structural element can be calculated by the strel (see 9.141) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions - number of sweeps.

9.50 gdilation3d - Dilation

This operator does successive dilations of the input image by the structural element supplied as the second input. The structural element can be calculated by the strel3d (see 9.142) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions - number of sweeps.

9.51 geometry - Crop the preset number of pixels from the image

This operator reduces dimensions of the input image. It crops pixels from each side of the image. The number of pixels is defined in the second input that can be generated by the crop (see 9.23) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif

9.52 geometry3d - Crop the preset number of pixels from the image

This operator reduces dimensions of the input image. It crops pixels from each side of the image. The number of pixels is defined in the second input that can be generated by the crop (see 9.23) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif

9.53 gerosion - Erosion

This operator does successive erosions of the input image by the structural element supplied as the second input. The structural element can be calculated by the strel (see 9.141) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions - number of sweeps.

9.54 gerosion3d - Erosion

This operator does successive erosions of the input image by the structural element supplied as the second input. The structural element can be calculated by the strel3d (see 9.142) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions - number of sweeps.

9.55 getp - Extract one plane from the stack

This operator extracts one plane from the stack.

input
1 image:.tif
output
1 image:.tif
parameters
Plane - the plane to extract.

9.56 gmag - Calculate the magnitude of the gradient

This operator calculates the magnitude of the gradient.

input
1 image:.tif
output
1 image:.tif

9.57 gopen - Morphological opening

This operator performs morphological opening which is the erosion followed by dilation using the structural element supplied as the second input. The structural element can be calculated by the strel (see 9.141) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions - number of sweeps.

9.58 gopen3d - Morphological opening

This operator performs morphological opening which is the erosion followed by dilation using the structural element supplied as the second input. The structural element can be calculated by the strel3d (see 9.142) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions - number of sweeps.

9.59 grid - Produce an image with the cartesian grid

This operator produces the image of the cartesian grid.

input
1 image:.tif
output
1 image:.tif
parameters
Number of bins - number of grid cells.

9.60 grid3d - Produce an image with the grid

This operator produces the image of the grid. The description of the shape is supplied as the second input. It can be produced by the qu3dinit (see 9.108) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Type - type of the grid - cartesian or elliptical.
Cell height - the height of the cell measured in per cent.
Cell width - the width of the cell measured in per cent.
Cell depth - the depth of the cell measured in per cent.
Offset - the offset of the center of the coordinate system measured in per cent. If set to 0 the center of the image will be the center of the coordinate system, if set to 0.5 the center of the image will be the center of the central cell.
Criterion - the allowed error.
Shape section - the name of the section in the second input that describes the shape of the object.

9.61 grid3d_i - Produce an image with the grid

This operator produces the image of the grid. The center of the object in the image is entered in the parameter dialog.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Type - type of the grid - cartesian or elliptical.
Cell height - the height of the cell measured in per cent.
Cell width - the width of the cell measured in per cent.
Cell depth - the depth of the cell measured in per cent.
Offset - the offset of the center of the coordinate system measured in per cent. If set to 0 the center of the image will be the center of the coordinate system, if set to 0.5 the center of the image will be the center of the central cell.
Criterion - the allowed error.
X Center - x coordinate of centroid.
Y Center - y coordinate of centroid.
Z Center - z coordinate of centroid.

9.62 halfsizes - Print the dimensions of the image

This operator prints dimensions of the image as a string of four numbers representing the distance in pixels from the image center to the borders.

input
1 image:.tif
output
1 text:.txt

The format of output file:
<halfsizes>
upper offset,lower offset, left offset, right offset - the distances in pixels from the image center to the borders
</halfsizes>

9.63 harris - Harris Edge detector

This operator implements the Harris algorithm for edge and corner detection.

input
1 image:.tif
output
1 image:.tif
parameters
Block size - size of window,
Aperture size - size of window to calculate the magnitude of gradient,
Free parameter - free parameter of the algorithm

9.64 heqm - Equalize histogram using mask

This operator performs the histogram equalization taking into account only those pixels that are "on" in the mask that comes from the second input.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.65 heq - Histogram equalization

This operator equalizes the histogram of the image. The idea is to spread out the histogram values to fill the entire range of the data type to enhance details that would be otherwise lost.

input
1 image:.tif
output
1 image:.tif

9.66 hues - Combine color channels into one image

This operator combines grayscale images of three color channels (Red, Green and Blue) to the one grayscale image in which each pixel equals the product of Hue and Saturation values in this pixel. The color channels can be extracted by the splitrgb (see 9.138) operator.

input
1 image:.tif
2 image:.tif
3 image:.tif
output
1 image:.tif

9.67 iapee - Visually correct the embryo orientation

This operator displays the image oriented according to the rules supplied in the second input and allows to flip and/or flop the image to correct the orientation. The output text file contains the list of needed operations.

input
1 image:.tif
2 text:.txt
output
1 text:.txt

The format of an output file:

<iapee>
-
reversecolumn or - if not needed
reverserows or - if not needed
</iapee>

9.68 invert - Invert the image

This operator inverts the grayscale values of all pixels in input image.

input
1 image:.tif
output
1 image:.tif

9.69 invert3d - Invert the image

This operator inverts the grayscale values of all pixels in input image.

input
1 image:.tif
output
1 image:.tif

9.70 lev - Extract the pixels with certain intensity

Those pixels that have the given intensity in the input image have the maximal intensity in the output image. The other pixels are "off".

input
1 image:.tif
output
1 image:.tif
parameters
Index - intensity.

9.71 lheq - Local histogram equalization

This operator performs histogram equalization separately for each pixel using the neighborhood defined by the structural element from the second input. The structural element can be calculated by the strel (see 9.141) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions- number of sweeps

9.72 lheq3d - Local histogram equalization

This operator performs histogram equalization separately for each pixel using the neighborhood defined by the structural element from the second input. The structural element can be calculated by the strel3d (see 9.142) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions- number of sweeps

9.73 lv3d - Rotate the stack around the vertical axis

This operator rotates the stack around the vertical axis.

input
1 image:.tif
output
1 image:.tif

9.74 m_ar_plus - Sum up the image dimensions

This operator sums up the image dimensions that are given by a string of four numbers which are the distances measured in pixels from the image center to its borders. The dimensions can be calculated by the halfsizes (see 9.62) operator.

input
1 text:.txt
output
1 text:.txt
parameters
Upper offset - number of pixels to add at the top,
Lower offset - number of pixels to add at the bottom,
Left offset - number of pixels to add at the left,
Right offset - number of pixels to add at the right.

9.75 m_ar_x - Multiply the image dimensions by a constant

This operator multiplies the image dimensions given by a string of four numbers which are the distances measured in pixels from the image center to its borders. The dimensions can be calculated by the halfsizes (see 9.62) operator. The constant is defined as a parameter.

input
1 text:.txt
output
1 text:.txt
parameters
Upper offset - multiplier for the number of pixels to add at the top,
Lower offset - multiplier for the number of pixels to add at the bottom,
Left offset - multiplier for the number of pixels to add at the left,
Right offset - multiplier for the number of pixels to add at the right.

9.76 match - Find objects matching the template

This operator finds in the binary image objects matching the template provided in the second input as the structural element. The structural element can be calculated by the strel (see 9.141) operator. Each matching object in the output binary image is marked with one bright pixel. This output can be used as the marker image for the reconstruct (see 9.115) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif

9.77 mask - Mask the image

This operator masks the first input image by the second one. The pixels that are "off" in the mask are "off" in the output image. Other pixels are kept unchanged from the input. The mask comes from the second input.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.78 max - Pixel by pixel maximum

This operator computes pixel by pixel maximum of three input images.

input
1 image:.tif
2 image:.tif
3 image:.tif
output
1 image:.tif

9.79 max2 - Pixel by pixel maximum of two images

This operator computes pixel by pixel maximum of two input images.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.80 max3d - Pixel by pixel maximum of the images in the stack

This operator computes pixel by pixel maximum of the images in the stack.

input
1 image:.tif
output
1 image:.tif

9.81 maxlsm - Pixel by pixel maximum of the channels in the stack

This operator computes pixel by pixel maximum of the channels in the stack.

input
1 image:.tif
output
1 image:.tif
parameters
Comma separated list - the channels.

9.82 mcrop - Crop an image manually

This operator reduces the dimensions of the input image. It crops the defined number of pixels from the each side of the image.

input
1 image:.tif
output
1 image:.tif
parameters
Upper offset - number of pixels to crop from the top,
Lower offset - number of pixels to crop from the bottom,
Left offset - number of pixels to crop from the left,
Right offset - number of pixels to crop from the right.

9.83 mcrop3d - Crop an image manually

This operator reduces the dimensions of the input image. It crops the defined number of pixels from the each side of the image.

input
1 image:.tif
output
1 image:.tif
parameters
Upper offset - number of pixels to crop from the top,
Lower offset - number of pixels to crop from the bottom,
Left offset - number of pixels to crop from the left,
Right offset - number of pixels to crop from the right.

9.84 median - Median filter

This operator computes a two dimensional median filter of a structural element over the given image. The structural element comes from the second input.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions- number of sweeps

9.85 median3d - Median filter

This operator computes a two dimensional median filter of a structural element over the given image. The structural element comes from the second input.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Repetitions- number of sweeps

9.86 minusabs - Subtract images

This operator produces the image of the absolute value of differences between pixel values of input images.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.87 mlsreg - Moving least squares registration of images

This operator registers two images using control points and moving least squares method.

input
1 image:.tif
2 image:.tif
2 image:.tif
output
1 image:.tif
parameters
Alpha - alpha coefficient,
Type - affine, similar or rigid.

9.88 movl2 - Combine two grayscale images into one color image

This operator combines two grayscale images into one color image. The colors for each input can be selected from the list.

input
1 image:.tif
2 image:.tif
output
1 image:.tif
parameters
Color 1 - color for the first input,
Color 2 - color for the second input.

9.89 movl3 - Combine three grayscale images into one color image

This operator combines three grayscale images into one color image. The colors for each input can be selected from the list.

input
1 image:.tif
2 image:.tif
3 image:.tif
output
1 image:.tif
parameters
Color 1 - color for the first input,
Color 2 - color for the second input,
Color 3 - color for the third input.

9.90 movl6 - Combine six grayscale images into one color image

This operator combines six grayscale images into one color image. The colors for each input can be selected from the list.

input
1 image:.tif
2 image:.tif
3 image:.tif
4 image:.tif
5 image:.tif
6 image:.tif
output
1 image:.tif
parameters
Color 1 - color for the first input,
Color 2 - color for the second input,
Color 3 - color for the third input,
Color 4 - color for the fourth input,
Color 5 - color for the fifth input,
Color 6 - color for the sixth input.

9.91 mpad - Pad the image with a preset number of pixels

This operator expands the dimensions of the input image. It adds the given number of pixels from the each side of the image.

input
1 image:.tif
output
1 image:.tif
parameters
Upper offset - number of pixels to add from the top,
Lower offset - number of pixels to add from the bottom,
Left offset - number of pixels to add from the left,
Right offset - number of pixels to add from the right.

9.92 mpad3d - Pad the image with a preset number of pixels

This operator expands the dimensions of the input image. It adds the given number of pixels from the each side of the image.

input
1 image:.tif
output
1 image:.tif
parameters
Upper offset - number of pixels to add from the top,
Lower offset - number of pixels to add from the bottom,
Left offset - number of pixels to add from the left,
Right offset - number of pixels to add from the right.

9.93 mslice3d - Visualize distance map

This operator visualizes the distance image supplied as the first input. The shape description is supplied as the second input. The resulting image contains equidistance surfaces.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Cell step - the distance between surfaces measured in per cent,
Direction - the direction in which steps are made to mark control points,
Shape section - the name of the section in the second input that describes the shape of the object.

9.94 mslicegcp3d - Find landmarks or control points for registration

This operator finds control points for registration using the distance image. The shape description is supplied as the second input. It works like mslice3d (see 9.93) but steps are made in one direction to produce equidistance surfaces and in the other direction to mark landmarks.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Cell step - the distance between surfaces measured in per cent,
Direction - the direction in which steps are made,
Slice direction - the direction in which steps are made,
Shape section - the name of the section in the second input that describes the shape of the object.
Cell height - the height of the cell measured in per cent.
Cell width - the width of the cell measured in per cent.
Cell depth - the depth of the cell measured in per cent.

9.95 mul - Multiply two images

This operator multiplies each data point in multiplier image by the corresponding data point in input image and returns the product in the corresponding data point of the output image.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.96 mul3d - Multiply two images

This operator multiplies each data point in multiplier image by the corresponding data point in input image and returns the product in the corresponding data point of the output image.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.97 nplot - Plot 2D graph

This operator produces the 2D graph in PNG or XFIG format using gnuplot. The input file should contain the table of two or more columns one of which represents the arguments and the others represent the function values in corresponding points. The input file can be generated by arcplot (see 9.10) or apro (see 9.4) or apron (see 9.5) operator. Several columns can be plotted at once. Data should be sorted with respect to the argument. This operator can not produce the legend but nplot2 (see 9.98) can.

input
1 text:.txt
output
1 image:.png
parameters
X column - number of the column with argument,
Y columns - the list of columns with function values,
Terminal - XFIG or PNG,
Line width - gnuplot option for the line width,
Line type - gnuplot option for the line type: lines, points, etc.

9.98 nplot2 - Plot 2D graph

This operator produces the 2D graph in PNG or XFIG format using gnuplot. The input file should contain the table of two or more columns one of which represents the arguments and others represent the function values at corresponding points. The input file can be generated by arcplot (see 9.10) or apro (see 9.4) or apron (see 9.5) operator. Several columns can be plotted at once. Data should be sorted in respect to the argument. This operator can produce the legend.

input
1 text:.txt
output
1 image:.png
parameters
X column - number of the column with argument,
Y columns - the list of columns with function values,
Titles - the list of titles, one title for each column,
Terminal - XFIG or PNG,
Line width - gnuplot option for the line width,
Line type - gnuplot option for the line type: lines, points, etc.,

9.99 pad - Pad the image

This operator expands the dimensions of the input image. It adds the pixels to the each side of the image. The number of pixels is defined in the second input that can be generated by the crop (see 9.23) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif

9.100 pad3d - Pad the image

This operator expands the dimensions of the input image. It adds the pixels to the each side of the image. The number of pixels is defined in the second input that can be generated by the crop (see 9.23) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif

9.101 plot_sp - Print the pixel values to the text file

This operator prints the values of pixels to the text file. Increment parameter n greater than 1 allows to print out only each nth pixel. Function parameter allows to print the actual values (eqn) or the natural logarithm (log) of the intensity.

input
1 image:.tif
output
1 text:.txt
parameters
Increment - counter increment,
Function - actual value or logarithm.

9.102 ppix - Print the pixel values along the line

This operator prints the values of pixels along the line to the text file. The line is defined as two parametric functions: r = a_r * t + b_r for row and c = a_c * t + b_c for column, where parameter t spans the interval [t₀,t_N]. The second output shows the image with the line superimposed on it.

input
1 image:.tif
output
1 text:.txt
2 image:.tif
parameters
ac - slope of parametric function for column,
bc - offset of parametric function for column,
ar - slope of parametric function for row,
br - offset of parametric function for row,
t0 - lower limit for parameter,
tN - upper limit for parameter.

9.103 prutik - Measure two distances visually

This operator shows the dialog window with the input image in which the user is allowed to mark two intervals that are then measured in pixels. The measurements are print in the output file.

input
1 image:.tif
output
1 text:.txt

9.104 pump3d - Convert distance image into volume

This operator converts an image into a stack using the distance map to determine the z coordinate.

input
1 image:.tif
output
1 image:.tif

9.105 pump3d_data - Convert distance image into volume with data

This operator converts an image into a stack using the distance map to determine the z coordinate. It also set the intensities in the stack according the second input.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.106 qu3d - Add quantitative data from another channel

This operator adds the quantitative data from another channel to the initialized storage. The image to extract data from is passed as the first input. The second input should contain the binary object mask. The initialized storage is supplied in the third input. The storage is initialized by the qu3dinit (see 9.108) operator.

input
1 image:.tif
2 image:.tif
3 text:.txt
output
1 text:.txt
parameters
Connectivity - 6 or 26,
Tag - String identifier for this channel.

9.107 qu3d2csv - Convert quantitative information to CSV format

This operator converts the quantitative data to CSV format.

input
1 text:.txt
output
1 text:.txt

9.108 qu3dinit - Initialize storage for quantitative data

This operator initializes the storage and adds the quantitative data from one channel. The image to extract data from is passed as the first input. The second input should contain the binary object mask.

input
1 image:.tif
2 image:.tif
output
1 text:.txt
parameters
Connectivity - 6 or 26,
Tag - String identifier for this channel.

9.109 qu3dtrans - Initialize storage for quantitative data

This operator filters the list of the objects and transforms their coordinates. The second input should contain the description of the shape of the object mask.

input
1 text:.txt
2 text:.txt
output
1 text:.txt
parameters
Shape section - the name of the section that describes the shape of the mask,
Percent - if set coordinates are converted to the per cent,
Center - if set coordinates are shifted to the center,
Min Volume - minimal number of pixels in the object,
Max Volume - maximal number of pixels in the object.

9.110 qumap3d - Paint the mask with quantitative data

This operator paints the binary mask with the intensities from quantitative data. The second input should contain the quantitative data produced by the qu3dinit (see 9.108) or the qu3d (see 9.106) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Connectivity - 6 or 26,
Channel - String identifier of the channel,
Index - The number starting from zero that determines the quantity in the list of measurements. Usually 0 means mean value, 1 - variation, 2 - standard deviation, 3 - maximum, 4 - minimum and 5 - median.

9.111 qumark3d - Paint the mask with quantitative data

This operator collapses the islands of bright pixels in the binary image to exactly one pixel. It is used to refine the landmarks for registration with mlsreg (see 9.87) operator.

input
1 image:.tif
output
1 image:.tif

9.112 qurelabel - Relabel objects after the registration of the mask

This operator labels each object in the registered mask with its index in the unregistered mask. Thus it is possible to compare quantitative data extracted from different images using the same mask registered to these images. The unregistered mask is supplied in the first input as binary image. The registered mask is supplied in the second input as the output of the qu3dinit (see 9.108) operator. The third input should contain the landmark of the registered image, and the forth input should contain the landmarks of the unregistered mask.

input
1 image:.tif
2 text:.txt
3 image:.tif
4 image:.tif
output
2 text:.txt
parameters
Alpha - alpha coefficient,
Type - affine, similar or rigid,
Connectivity - 6 or 26.

9.113 raw - Make tiff from raw

This operator reads raw image and writes it in tiff format.

input
1 image:.tif
output
1 image:.tif
parameters
Columns - number of columns in the image,
Rows - number of rows in the image,
Bps - number of bits per pixel.

9.114 rec3dbp - Morphological reconstruction

This operator performs morphological reconstruction of the stack from the marker image. The specified plane of the stack is compared to the marker image.

input
1 image:.tif
2 marker:.tif
output
1 image:.tif
parameters
Connectivity - 6 or 26,
Plane - the plane of the stack to compare.

9.115 reconstruct - Morphological reconstruction

This operator performs morphological reconstruction of the image from the marker image.

input
1 image:.tif
2 marker:.tif
output
1 image:.tif

9.116 reconstruct3d - Morphological reconstruction

This operator performs morphological reconstruction of the image from the marker image.

input
1 image:.tif
2 marker:.tif
output
1 image:.tif

9.117 regmax - Regional maxima

This operator finds regional maxima.

input
1 image:.tif
output
1 image:.tif
parameters
Minimal number of pixels - Minimal number of pixels in the object,
Maximal number of pixels - Maximal number of pixels in the object,
Minimal number of blobs - Minimal number of objects,
Connectivity - 4 or 8.

9.118 regmin - Regional minima

This operator finds regional minima.

input
1 image:.tif
output
1 image:.tif
parameters
Minimal number of pixels - Minimal number of pixels in the object,
Maximal number of pixels - Maximal number of pixels in the object,
Minimal number of blobs - Minimal number of objects,
Connectivity - 4 or 8.

9.119 restack3d - Remove planes from the stack

This operator removes planes from the stack with the specified step.

input
1 image:.tif
output
1 image:.tif
parameters
Step - planes are removed with this step.

9.120 revcol - Reverse columns

This operator reverses columns in the image. Thus the leftmost pixel in each row becomes the rightmost one and so on.

input
1 image:.tif
output
1 image:.tif

9.121 revcol3d - Reverse columns

This operator reverses columns in the image. Thus the leftmost pixel in each row becomes the rightmost one and so on.

input
1 image:.tif
output
1 image:.tif

9.122 revrow - Reverse rows

This operator reverses rows in the image. Thus the uppermost pixel in each column becomes the lowest and so on.

input
1 image:.tif
output
1 image:.tif

9.123 revrow3d - Reverse rows

This operator reverses rows in the image. Thus the uppermost pixel in each column becomes the lowest and so on.

input
1 image:.tif
output
1 image:.tif

9.124 robel - Produce the image of round strip

This operator produces the image of round strip that includes all blobs from the second input. The first input is used to determine the center of polar coordinates. The third input contains the list of points in polar coordinates that determine the inner and outer borders of the round strip. This file can be generated by the ropri (see 9.127) operator. The pixel in the output image is "on" if it is "on" in the second input and its coordinates belong to the round strip.

input
1 image:.tif
2 image:.tif
3 text:.txt
output
1 image:.tif

9.125 rogri - Divide the image into sectors

This operator divides the image from the second input into sectors. The pixels are switched off in the output if their polar angle is closer than the predefined value (Accuracy) to the sector delimiter.

input
1 image:.tif
2 image:.tif
output
1 image:.tif
parameters
Number of bins - number of sectors to produce,
Accuracy

9.126 ropol - Print the pixel values

This operator prints the pixel values from the third input to the text file in polar coordinates. The center of the coordinate system is calculated from the first input. The second input is used as the mask. Function parameter allows to print the actual values (eqn) or the natural logarithm (log) of the intensity.

input
1 image:.tif
2 image:.tif
3 image:.tif
output
1 text:.txt
parameters
Function - the actual value (eqn) or the natural logarithm (log).

9.127 ropri - Print the landmarks of the borders of the round strip

This operator calculates the list of points in polar coordinates that determines the inner and outer borders of the round strip. The center of the polar coordinates is calculated from the first input. The second input is the list of blobs with polar coordinates of centroids that can be calculated by the blo2pol (see 9.13) operator. The output is sorted with respect to the polar angle.

input
1 image:.tif
2 text:.txt
output
1 text:.txt

9.128 rotate - Calculate the rotation angle

This operator computes the rotation angle using invariant moments and rotates the image. The text file with calculated angle is the second output.

input
1 image:.tif
output
1 image:.tif
2 text:.txt

9.129 rv3d - Rotate the stack around the vertical axis

This operator rotates the stack around the vertical axis in the direction opposite to that used in the lv3d (see 9.73) operator.

input
1 image:.tif
output
1 image:.tif

9.130 save - Save file

This operator saves an input file in the server "public" folder with assigned name.

input
1 image:.tif

9.131 setp - Set one plane in the stack

This operator sets one plane in the stack from the second input.

input
1 image:.tif
output
1 image:.tif
parameters
Plane - the plane to set.

9.132 shape - Characterize the shape

This operator outputs the description of the shape.

input
1 image:.tif
output
1 image:.tif

9.133 shape3d - Characterize the shape

This operator outputs the description of the shape.

input
1 image:.tif
output
1 image:.tif
parameters
Connectivity - 6 or 26.

9.134 shrink - Shrink image via pixel subsampling

This operator reduces the size of the input image using pixel subsampling.

input
1 image:.tif
output
1 image:.tif
parameters
Scale - the scaling factor from 0 to 1.

9.135 shrink3d - Shrink image via pixel subsampling

This operator reduces the size of the input image using pixel subsampling.

input
1 image:.tif
output
1 image:.tif
parameters
Scale - the scaling factor from 0 to 1.

9.136 solo - Extract quantitative information

This operator calculates the given statistical estimator of pixel intensities for each blob, listed in the first input that can be generated by the blob operator. The statistical estimators are calculated for each of five input images – channels (inputs 2 – 6). They are placed in the corresponding column of the output file. The mean value, median value, maximum, minimum, number of pixels, variation or standard deviation can be calculated for blobs (nuclear), their surroundings (outnuc) and the union of them (energid). The ratio of variances in pixel values between and within these two classes (varbc) can be calculated if outnuc is selected as the Mask parameter for this channel.

input
1 text:.txt
2 image:.tif
3 image:.tif
4 image:.tif
5 image:.tif
6 image:.tif
output
1 text:.txt
parameters
The following parameters are defined for each of five input channels:
Mask - nuclear, energid or outnuc,
Stat - mean, median, max, min, stdev, var, area or varbc,
P - one letter label.

9.137 splitlsm - Write each color in the separate file

This operator splits the input color image into three grayscale images, one for each color channel.

input
1 image:.tif
output
1 image:.tif
2 image:.tif
3 image:.tif

9.138 splitrgb - Write each color in the separate file

This operator splits the input color image into three grayscale images, one for each color channel.

input
1 image:.tif
output
1 image:.tif
2 image:.tif
3 image:.tif

9.139 sselect - Select objects according to the shape

This operator filters objects in the binary image according to the shape. The template is provided in the second input as the binary image. The comparison is insensitive to the rotation, translation and scaling.

input
1 image:.tif
2 image:.tif
output
1 image:.tif
parameters
Max segment - maximal number of pixels in the object,
Min segment - minimal number of pixels in the object,
Rule - accept or reject,
Criterion - maximal allowed error,
Connectivity - 4 or 8.

9.140 sselect3d - Select objects according to the shape

This operator filters objects in the binary image according to the shape. The template is provided in the second input as the binary image. The comparison is insensitive to the rotation, translation and scaling.

input
1 image:.tif
2 image:.tif
output
1 image:.tif
parameters
Max segment - maximal number of pixels in the object,
Min segment - minimal number of pixels in the object,
Rule - accept or reject,
Criterion - maximal allowed error,
Connectivity - 6 or 26.

9.141 strel - Structural element

This operator generates a structural element file.

input
0 output
1 text:.txt
parameters
Window width - in pixels,
Window height - in pixels,
Shape - disk or square.

9.142 strel3d - Structural element

This operator generates a structural element file.

input
0 output
1 text:.txt
parameters
Window width - in pixels,
Window height - in pixels,
Window depth - in pixels,
Shape - disk or square,
Shape - disk or square.

9.143 strel3dw - Structural element

This operator generates a structural element file.

input
0 output
1 text:.txt
parameters
Window width - in pixels,
Window height - in pixels,
Window depth - in pixels,
Window wall - in pixels,
Shape - disk or square,
Shape - disk or square.

9.144 surf2vol - Draw triangulated surface

This operator draws triangulated surface.

input
1 text:.txt
output
1 image:.tif

9.145 surf3d - Produce triangulated surface

This operator produces triangulated surface.

input
1 image:.tif
output
1 text:.txt
parameters
Scale column - horizontal scale,
Scale row - vertical scale,
Scale plane - scale in z direction,
Maximal penalty of edge removal - for surface refinement,
Minimal angle - for surface refinement,
Format - vtk, oogl, ooglb or gts.

9.146 surf3dfull - Produce triangulated surface with full control

This operator produces triangulated surface.

input
1 image:.tif
output
1 text:.txt
parameters
Scale column - horizontal scale,
Scale row - vertical scale,
Scale plane - scale in z direction,
Maximal penalty of edge removal - for surface refinement,
Minimal angle - for surface refinement,
Format - vtk, oogl, ooglb or gts,
Step x - in pixels,
Step y - in pixels,
Step z - in pixels,
Function - cartesian, tetra, tetra_bounded or tetra_bcl.

9.147 threshb - Threshold pixel values in each blob

This operator generates a binary image by thresholding the input image. Pixel values greater than the cutoff value are set to 255 in the output image. Pixel values less or equal to the cutoff are set to 0. The cutoff value is calculated by Otsu’s method in each blob contained in the second input. Otsu’s method chooses the threshold to minimize the intraclass variance of black and white pixels [3].

input
1 image:.tif
2 text:.txt
output
1 image:.tif

9.148 threshold - Threshold pixel values

This operator generates a binary image by thresholding the input image. Pixel values greater than the cutoff value are set to 255 in the output image. Pixel values less or equal to the cutoff are set to 0. The cutoff value can be specified by a user or calculated by Otsu’s method, which chooses the threshold to minimize the intraclass variance of black and white pixels [3]. Second output gives the actual threshold used.

input
1 image:.tif
output
1 image:.tif
2 text:.txt
parameters
Threshold level - the threshold value,
Method - plain or otsu,
Process? - do actual transformation or not.

9.149 threshold3d - Threshold pixel values

This operator generates a binary image by thresholding the input image. Pixel values greater than the cutoff value are set to 255 in the output image. Pixel values less or equal to the cutoff are set to 0. The cutoff value can be specified by a user or calculated by Otsu’s method, which chooses the threshold to minimize the intraclass variance of black and white pixels [3]. Second output gives the actual threshold used.

input
1 image:.tif
output
1 image:.tif
2 text:.txt
parameters
Threshold level - the threshold value,
Method - plain or otsu,
Process? - do actual transformation or not.

9.150 turn - Rotate image on given angle

This operator rotates image to a given angle (second input) that can be calculated by the rotate (see 9.128) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif

9.151 turn3d - Rotate image on given angle

This operator rotates image to a given angle (second input) that can be calculated by the rotate (see 9.128) operator.

input
1 image:.tif
2 text:.txt
output
1 image:.tif

9.152 tv3d - Rotate the stack around the horizontal axis

This operator rotates the stack around the horizontal axis.

input
1 image:.tif
output
1 image:.tif

9.153 vaff - Linear combination of two images pixel by pixel

This operator computes a linear combination of two images pixel by pixel.

Output = <coeff 1> * input_1 + <coeff 2> * input_2 + <coeff 3>;

input
1 image:.tif
2 image:.tif
output
1 image:.tif
parameters
Coeff 1,
Coeff 2,
Coeff 3.

9.154 vavg - Average images pixel by pixel

This operator averages two images pixel by pixel.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.155 vmabs - Subtract images

This operator produces the image of the absolute value of differences between pixel values of input images.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.156 vmax - Pixel by pixel maximum of two images

This operator computes pixel by pixel maximum of two input images.

input
1 image:.tif
2 image:.tif
output
1 image:.tif

9.157 vrgb - Combine three grayscale images into one color image

This operator combines three grayscale images into one color image.

input
1 image:.tif
2 image:.tif
3 image:.tif
output
1 image:.tif

9.158 vrmbg - Remove background signal

This operator removes background signal form the image. Background is to be estimated quantitatively and its mean and standard deviation is to be present in the appropriate section in the second input. The value <Bgr mean coeff>*<bgr mean> + <bgr stdev coeff>*<bgr stdev> is subtracted from each pixel.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Bgr mean coeff - the coefficient for the mean value of background signal,
Bgr section - the section with measurements in the second input,
Bgr stdev coeff - the coefficient for the standard deviation,
Bgr data - the string identifier for the measurements.

9.159 vrmbg_1 - Remove background signal

This operator removes background signal form the image. The mean and standard deviation of it is to be provided by the user. The value <Bgr mean coeff>*<bgr mean> + <bgr stdev coeff>*<bgr stdev> is subtracted from each pixel.

input
1 image:.tif
2 text:.txt
output
1 image:.tif
parameters
Bgr mean coeff - the coefficient for the mean value of background signal,
Bgr mean - the mean value of background signal,
Bgr stdev coeff - the coefficient for the standard deviation,
Bgr stdev - the standard deviation.

9.160 vstrel - Convert structural element to the image

This operator convert structural element to the image.

input
1 text:.txt
output
1 image:.tif

9.161 vstrel3d - Convert structural element to the image

This operator convert structural element to the image.

input
1 text:.txt
output
1 image:.tif

9.162 vtxt - Convert the stack to text file

This operator converts the binary image stack to the text file.

input
1 image:.tif
output
1 text:.txt
parameters
Format - XYZ or VRML,
Connectivity - 6 or 26.

9.163 vvarbc3d - Calculates the ratio of variances

This operator calculates the ratio of variancies of pixel values in the image between and within two classes. The pixels of the first class belong to blobs, the second class includes all the pixels that belong to surroundings. The input is the list of blobs and can be calculated by the qu3dinit (see 9.108) operator.

input
1 text:.txt
output
1 text:.txt
parameters
Output section - the name of the output section,
Class 1 section - the name of the section that describes first class,
Class 1 data - the string identifier of the data that describes first class,
Class 2 section - the name of the section that describes second class,
Class 2 data - the string identifier of the data that describes second class.

9.164 zscale3d - Scale the stack in z direction

This operator scales the stack in z direction.

input
1 image:.tif
output
1 image:.tif
parameters
Scale - the scale.