DESCRIPTION

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.

-e, --functional-overlay [rgbImageFileName,maskImageFileName,<alpha=1>]

A functional overlay can be specified using both and rgb image and a mask specifying where that rgb image should be applied. Both images must have the same image geometry as the input image. Optionally, an alpha parameter can be specified.Note that more than one functional overlays can be rendered, the order in which they are specified on the command line matters, and rgb images are assumed to be unsigned char [0,255].

-o, --output tiledMosaicImage

The output is the tiled mosaic image. Without an RGB overlaywe do not alter the intensity values of the input image. Therefore, the output suffix needs to be associated with a format that supports float images (not .jpg or .png). If one or more RGB overlays are supported then we rescale the input image intensities to also be in the range of [0,255] which permits a .png or .jpg output.

-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/x/y/(z)

Specifies the direction of the slices. This can be based on the how the image is stored in memory or can be based on how the image is aligned in physical space. If no direction is specified, the z-direction (axial?) 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