Mosaic Exporter User Manual

Introduction

Command Line

The command line version of the Mosaic Exporter is invoked using either a terminal (on Unix type systems) or using the "Command Prompt" on Windows. Simply invoking the command line utility with no arguments will produce a message that displays all the necessary arguments.
[mjackson@workstation] $ MosaicExporter
Required Parameters:
  --help                    Produce help message
  --help                    Produce help message
  -i [ --inputfile ] arg    MXA File to be used as input
  -r [ --recname ] arg      Name of the Data Record to Export
  -s [ --sliceStart ] arg   The value of the starting slice to export
  -e [ --sliceEnd ] arg     The value of the ending slice to export
  -l [ --logfile ] arg      Path to a log file to write output messages to.
  -L [ --listRecords ] arg  List the possible Data Model Records for the given MXA file
  -o [ --outputPrefix ] arg The path to where the image files will be written.
  -d [ --description ] arg  Description to be used for the tiff_tag 'IMAGE_DESCRIPTION'
  -z [ --rescale ] arg      Scaling Factor - 100.0 is full size. 50.0 is half  the size
  --voiOrigin               Use VOI Origin
  -x [ --originx ] arg      X Origin of the VOI
  -y [ --originy ] arg      Y Origin of the VOI
  --voiSize                 Use VOI Size
  -w [ --width ] arg        Width (Microns) of VOI
  -h [ --height ] arg       Height (Microns) of VOI
  --working_volume          Compute the largest Volume that would encompass the maximum area from each slice.
  -v [ --verbose ]          Verbose Output

Argument Details

-i [ --inputfile ] This is the complete path to the MXA data file that holds the RoboMet data to be processed.

-o [--outputprefix] The path + partial file name that will start each exported slice. This can be a path + a partial file name or just a partial filename. If a relative path is give then it is relative to the directory where the executale is being run from. Some examples that this input parameter can have are:

  /tmp/MyExperiment_
  C:\Data\MyExperiment-Images\MyExperimentImage-
The slice number and ".tif" will be appended to the argument to form the full path name. Please note that you are responsible for making sure that any intermediate directories are already created.

-r [ --recname ] You will need to know the name of the MXA Data Record that represents the image that you would like to process. Typically this is "Zeiss Image".

-d [ --description ] A short sentence describing the data. This is placed in the TIFF_COMMENT section of the tif header. (Currently not used).

-s [ --sliceStart ] The first slice of data to export

-e [ --sliceEnd ] The last slice of data to export

-z [ --rescale ] Rescale the images exported by the given percent. 100.0 is full size, 50.0 is half size, 200.0 is double the size of the original

--voiOrigin Use this flag followed by the -x (--originx) and -y (--originy) to denote that a specified volume of interest is to be used. If this parameter left out then the entire mosaic is exported and alignment of each slice is only as good as the original data aquisition. Arguments for these parameters are given in microns. For example:

 --voiOrigin -x 46590 -y 47892
Will export a mosaic where the corner (Upper Left Typically) will be at the coordinate specified. This may result in mosaics thare are partially "black" due to no data being available. This is usually used in combination with the --voiSize argument.

--voiSize Use this flag followed by the -w (--width) and -h (--height) flags to specify the size in Microns of the Mosaic being exported. If you would like an aligned set of images then you must use this parameter along with the --voiOrigin parameter.

-l [ --logfile ] The path to a file to store debugging messages into.

-L [--listRecords] Returns a list of the MXA Data Records in the MXA File.

--working_volume Calculates the working volume of the data set which is the largest volume that contains valid data.

-v [ --verbose ] Determines how many debugging messages are written to the log file

GUI Application

To use the GUI version of the R3DMosaicExporter double click the R3DMosaicExporter.exe (Windows), R3DMosaicExporter.app (OS X) or R3DMosaicExporter (Linux).

R3DMosaicExporter-1.jpg

The R3DMosaicExporter GUI Application Showing the Main Input/Output Tab

Simply fill out the text fields and use the buttons to select the various outputs. When you are ready to export your data, click the "Export" button and wait for the process to complete. You may click cancel at any time during the alignment process.

If you only want a subvolume, need more verbose output or want to resize the images being produced you can click the "Options" tab to set those variables.

R3DMosaicExporter-2.jpg

The R3DMosaicExporter GUI Application Showing the Options Tab

If you would like to calculate the working volume of the data set then use the "Working Volume" tab.

R3DMosaicExporter-3.jpg

The R3DMosaicExporter GUI Application Showing the Working Volume Calculation Tab


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