Module: Align Mosaic Blocks ()

Description:

The Align Mosaic Blocks module is for aligning the blocks of a mosaic. During the acquisition of the image blocks of a mosaic, it may happen that the blocks are not perfectly aligned. This module computes the best adjustment between overlapping blocks, i.e., finds the translations between each pair of blocks that minimizes the difference in the common part of the two images.

Press the Apply button to start the computation.

Connections:

Data [required]
Mosaic

Ports:

Mosaic Name

Stores the filename of the final mosaic and of the temporary files: during the planar alignment, the module creates 2D projections of the image blocks. These projections are stored with the extension "nb.mip.am" where nb represents the number of the block in the mosaic.

Translation

Max Trans. X (pixels)

Maximum value of translation to apply in the X direction (in pixels).

X Image Units Value

Gives the corresponding value in image units (for example, if the voxel size is given in micrometers, gives the maximum translation in micrometers).

Max Trans. Y (pixels)

Maximum value of translation to apply in the Y direction (in pixels).

Y Image Units Value

Gives the corresponding value in image units (for example, if the voxel size is given in micrometers, gives the maximum translation in micrometers).

Max Trans. Z (pixels)

Maximum value of translation to apply in the Z direction (in pixels).

Z Image Units Value

Gives the corresponding value in image units (for example, if the voxel size is given in micrometers, gives the maximum translation in micrometers).

Alignment Options

Alignment

Performs a planar and/or a vertical alignment. If planar is checked, makes a 2D projection of each image (on XY plane), and finds the best planar translation between each image. If vertical is checked, then finds the vertical component of the translation.

Similarity Measure

This port allows you to select either the SSD (sum of squared differences) or the correlation method for computing how well the blocks are aligned.