1 Team
2 License
3 Terms, Abbreviations and Notation
4 Scheduler
5 Installation of a binary packages
 5.1 Installation on Fedora 13 and later
 5.2 Installation on generic GNU/Linux
 5.3 Installation on MS Windows and Mac OS X
 5.4 System requirements
6 Usage
 6.1 Main window
 6.2 Graphical scenario builder
 6.3 Constructing a new workspace
 6.4 Work with existing workspace
 6.5 Compiling the workflow
 6.6 Several workspaces or several datatsets
7 AP format
8 Examples
 8.1 "orient" - Correct orientation of Drosophila embrios
 8.2 "expr" - Extract quantitative information on gene expression
 8.3 "k167" - Identify cells
 8.4 "nuclei3d" - Identify nuclei in 3D stack
9 List of Workflow Modules
 9.1 align - Generate rules to correct the embryo orientation
 9.2 andif - Anisotropic diffusion
 9.3 apee - Correct orientation of embryo
 9.4 apro - Filter the table
 9.5 apron - Filter the data
 9.6 apsc - Check the orientation of embryo
 9.7 ar_minus - Subtract the image dimensions
 9.8 ar_plus - Sum up the image dimensions
 9.9 ar_x - Multiply the image dimensions by a constant
 9.10 arcplot - Average the intensities over bins
 9.11 avg - Average images pixel by pixel
 9.12 avg2 - Average images pixel by pixel
 9.13 blo2pol - Convert the coordinates to polar coordinates
 9.14 blob - Extract the objects from the binary image
 9.15 bolb - Draw an image of the blobs
 9.16 bolin - Draw an image of the selected blob
 9.17 canny - Canny Edge detector
 9.18 chemar - Check the orientation of the Drosophila embryo
 9.19 chole - Closing of holes
 9.20 chole3d - Closing of holes
 9.21 cmove - Move data using curl
 9.22 cmove_i - Move data using curl
 9.23 crop - Crop image
 9.24 curlup - Move data using curl
 9.25 cwtsd - Watershed transform
 9.26 cwtsd3d - Watershed transform
 9.27 decbsup - Blind deconvolution
 9.28 decbsup_i - Blind deconvolution
 9.29 decinv - Inverse filter
 9.30 decinv_i - Inverse filter
 9.31 decsup - Richardson-Lucy deconvolution
 9.32 decsup_i - Richardson-Lucy deconvolution
 9.33 dectm - Tikhonov-Miller deconvolution
 9.34 dectm_i - Tikhonov-Miller deconvolution
 9.35 decwiener - Wiener filter
 9.36 decwiener_i - Wiener filter
 9.37 despekle - Reduce speckle noise in the input image
 9.38 despekle3d - Reduce speckle noise in the input image
 9.39 diglsm - Distance transform
 9.40 distance - Distance transform
 9.41 distance3d - Distance transform
 9.42 edge - Edge detection
 9.43 edge3d - Edge detection
 9.44 expand - Expand image via pixel replication
 9.45 expand3d - Expand image via pixel replication
 9.46 fill - Fill the holes
 9.47 gclose - Morphological closing
 9.48 gclose3d - Morphological closing
 9.49 gdilation - Dilation
 9.50 gdilation3d - Dilation
 9.51 geometry - Crop the preset number of pixels from the image
 9.52 geometry3d - Crop the preset number of pixels from the image
 9.53 gerosion - Erosion
 9.54 gerosion3d - Erosion
 9.55 getp - Extract one plane from the stack
 9.56 gmag - Calculate the magnitude of the gradient
 9.57 gopen - Morphological opening
 9.58 gopen3d - Morphological opening
 9.59 grid - Produce an image with the cartesian grid
 9.60 grid3d - Produce an image with the grid
 9.61 grid3d_i - Produce an image with the grid
 9.62 halfsizes - Print the dimensions of the image
 9.63 harris - Harris Edge detector
 9.64 heqm - Equalize histogram using mask
 9.65 heq - Histogram equalization
 9.66 hues - Combine color channels into one image
 9.67 iapee - Visually correct the embryo orientation
 9.68 invert - Invert the image
 9.69 invert3d - Invert the image
 9.70 lev - Extract the pixels with certain intensity
 9.71 lheq - Local histogram equalization
 9.72 lheq3d - Local histogram equalization
 9.73 lv3d - Rotate the stack around the vertical axis
 9.74 m_ar_plus - Sum up the image dimensions
 9.75 m_ar_x - Multiply the image dimensions by a constant
 9.76 match - Find objects matching the template
 9.77 mask - Mask the image
 9.78 max - Pixel by pixel maximum
 9.79 max2 - Pixel by pixel maximum of two images
 9.80 max3d - Pixel by pixel maximum of the images in the stack
 9.81 maxlsm - Pixel by pixel maximum of the channels in the stack
 9.82 mcrop - Crop an image manually
 9.83 mcrop3d - Crop an image manually
 9.84 median - Median filter
 9.85 median3d - Median filter
 9.86 minusabs - Subtract images
 9.87 mlsreg - Moving least squares registration of images
 9.88 movl2 - Combine two grayscale images into one color image
 9.89 movl3 - Combine three grayscale images into one color image
 9.90 movl6 - Combine six grayscale images into one color image
 9.91 mpad - Pad the image with a preset number of pixels
 9.92 mpad3d - Pad the image with a preset number of pixels
 9.93 mslice3d - Visualize distance map
 9.94 mslicegcp3d - Find landmarks or control points for registration
 9.95 mul - Multiply two images
 9.96 mul3d - Multiply two images
 9.97 nplot - Plot 2D graph
 9.98 nplot2 - Plot 2D graph
 9.99 pad - Pad the image
 9.100 pad3d - Pad the image
 9.101 plot_sp - Print the pixel values to the text file
 9.102 ppix - Print the pixel values along the line
 9.103 prutik - Measure two distances visually
 9.104 pump3d - Convert distance image into volume
 9.105 pump3d_data - Convert distance image into volume with data
 9.106 qu3d - Add quantitative data from another channel
 9.107 qu3d2csv - Convert quantitative information to CSV format
 9.108 qu3dinit - Initialize storage for quantitative data
 9.109 qu3dtrans - Initialize storage for quantitative data
 9.110 qumap3d - Paint the mask with quantitative data
 9.111 qumark3d - Paint the mask with quantitative data
 9.112 qurelabel - Relabel objects after the registration of the mask
 9.113 raw - Make tiff from raw
 9.114 rec3dbp - Morphological reconstruction
 9.115 reconstruct - Morphological reconstruction
 9.116 reconstruct3d - Morphological reconstruction
 9.117 regmax - Regional maxima
 9.118 regmin - Regional minima
 9.119 restack3d - Remove planes from the stack
 9.120 revcol - Reverse columns
 9.121 revcol3d - Reverse columns
 9.122 revrow - Reverse rows
 9.123 revrow3d - Reverse rows
 9.124 robel - Produce the image of round strip
 9.125 rogri - Divide the image into sectors
 9.126 ropol - Print the pixel values
 9.127 ropri - Print the landmarks of the borders of the round strip
 9.128 rotate - Calculate the rotation angle
 9.129 rv3d - Rotate the stack around the vertical axis
 9.130 save - Save file
 9.131 setp - Set one plane in the stack
 9.132 shape - Characterize the shape
 9.133 shape3d - Characterize the shape
 9.134 shrink - Shrink image via pixel subsampling
 9.135 shrink3d - Shrink image via pixel subsampling
 9.136 solo - Extract quantitative information
 9.137 splitlsm - Write each color in the separate file
 9.138 splitrgb - Write each color in the separate file
 9.139 sselect - Select objects according to the shape
 9.140 sselect3d - Select objects according to the shape
 9.141 strel - Structural element
 9.142 strel3d - Structural element
 9.143 strel3dw - Structural element
 9.144 surf2vol - Draw triangulated surface
 9.145 surf3d - Produce triangulated surface
 9.146 surf3dfull - Produce triangulated surface with full control
 9.147 threshb - Threshold pixel values in each blob
 9.148 threshold - Threshold pixel values
 9.149 threshold3d - Threshold pixel values
 9.150 turn - Rotate image on given angle
 9.151 turn3d - Rotate image on given angle
 9.152 tv3d - Rotate the stack around the horizontal axis
 9.153 vaff - Linear combination of two images pixel by pixel
 9.154 vavg - Average images pixel by pixel
 9.155 vmabs - Subtract images
 9.156 vmax - Pixel by pixel maximum of two images
 9.157 vrgb - Combine three grayscale images into one color image
 9.158 vrmbg - Remove background signal
 9.159 vrmbg_1 - Remove background signal
 9.160 vstrel - Convert structural element to the image
 9.161 vstrel3d - Convert structural element to the image
 9.162 vtxt - Convert the stack to text file
 9.163 vvarbc3d - Calculates the ratio of variances
 9.164 zscale3d - Scale the stack in z direction
10 ProStack and Omero
 10.1 System requirements
 10.2 List of modules
 10.3 file - Browse the OMERO repository
 10.4 omero_exporter - Get image from OMERO server
 10.5 omero_exporter_i - Get selected image from OMERO server
 10.6 omero_importer - Import an image to OMERO server
 10.7 Step-by-step how-to
11 ProStack Server Deployment Guide
 11.1 System requirements
 11.2 Architecture
 11.3 Installation
 11.4 Server Configuration
 11.5 Client Configuration
 11.6 ProStack Server Component and SELinux