Zeiss Lightsheet Z.1, Operating Manual

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CHAPTER 4 - SYSTEM OPERATION
Lightsheet Z.1 Left Tool Area and Hardware Control Tools Carl Zeiss
02/2013 000000-1790-528 111
3.3.12 Processing – Stitch
Licensing Instrument
standard  optional  LSM  ELYRA Lightsheet Z.1
Tool accepts image data recorded data recorded with the acquisition tool Tile Scan
(incl. combinations with other multi-dimensional acquisition tools). Images recorded
in SIM mode on ELYRA (SIM data) must be processed with the tool
Structured
Illumination before stitching. For optimal results, image data should have some
degree of lateral overlap. See full description of tool for details.
With this function tiled images acquired with
Versions of ZEN 2012 and upwards and the tiling
function can be stitched together in 2D and 3D.
Select a tiled image (or stack) with the
Select
button (Fig. 161).
The
Correlation Threshold is defining the
accuracy with which the algorithm detects
similarities in the adjacent image planes.
If a 3D tile scan image has been acquired (Tile Scan
combined with Z-Stack) then additional functions
for the stitching procedure are available.
Ignore Z Correction will in some cases reveal
better results for the 3D stitch. Depending on the
image data the last step of the stitch algorithm,
which makes a correction of the Z-Stacks in Z
looking at the overall image, can lead to unwanted
shifts of the stacks in Z. This can be avoided when
this option is checked.
Calculate Topography provides a topographic
image of the 3D stitched image data. This
calculation can be done in several modes.
First / Last maximum
•
Select First maximum to calculate the topography surface by using the first maximum coming from
the top. This mode provides better result for surfaces of semitransparent materials with inclusions of
higher reflectivity or transparent multi-layers with subsurface layers of higher signal intensity.
•
Select Last maximum to calculate the topography surface by using the last maximum coming from
the top.
Fig. 161 Processing – Stitch