COMMAND:¶

CreateTiledMosaic

Render a 3-D image volume with optional Rgb overlay.

OPTIONS:¶

-i, --input-image inputImageFilename

Main input is a 3-D grayscale image.

-r, --rgb-image rgbImageFilename

An optional Rgb image can be added as an overlay. It must have the same image geometry as the input grayscale image.

-x, --mask-image maskImageFilename

Specifies the ROI of the RGB voxels used.

-a, --alpha value

If an Rgb image is provided, render the overlay using the specified alpha parameter.

-o, --output tiledMosaicImage

The output consists of the tiled mosaic image.

-t, --tile-geometry RxC

The tile geometry specifies the number of rows and columns in the output image. For example, if the user specifies '5x10', then 5 rows by 10 columns of slices are rendered. If R < 0 and C > 0 (or vice versa), the negative value is selected based on direction.

-d, --direction 0/1/2

Specifies the direction of the slices. If no direction is specified, the direction with the coarsest spacing is chosen.

-p, --pad-or-crop padVoxelWidth

[padVoxelWidth,<constantValue=0>] [lowerPadding[0]xlowerPadding[1],upperPadding[0]xupperPadding[1],constantValue]

The user can specify whether to pad or crop a specified voxel-width boundary of each individual slice. For this program, cropping is simply padding with negative voxel-widths. If one pads (+), the user can also specify a constant pad value (default = 0). If a mask is specified, the user can use the mask to define the region, by using the keyword "mask" plus an offset, e.g. "-p mask+3".

-s, --slices Slice1xSlice2xSlice3...

numberOfSlicesToIncrement [numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]

This option gives the user more control over what slices to use for rendering. The user can specify specific slices for a particular order. Alternatively the user can specify the number slices to increment with the optional specification of which slices to start and end the sequence. A negative value for the numberOfSlicesToIncrement causes rendering in the reverse order. For the third option, minSlice < maxSlice. If a mask is specified, the user can use the mask to define the region, by using the keyword "mask" plus an offset, e.g. "-s [1,mask-3,200]".For the third option, minSlice < maxSlice.

-f, --flip-slice flipXxflipY

Flip individual slice images horizontally and/or vertically, specified e.g. as '0x1' or '1x1'.

-g, --permute-axes doPermute

Permute (or swap) the axes of the individual slice images.

-h

Print the help menu (short version).

--help

Print the help menu. <VALUES>: 1