Zeiss Lightsheet Z.1, Operating Manual

Page: 326 / 427

CHAPTER 4 - SYSTEM OPERATION
Carl Zeiss Left Tool Area and Hardware Control Tools Lightsheet Z.1
156 000000-1790-528 02/2013
3.3.19.1 Remove Structure
•
Activate
Remove structures
in the
ICS
tool. The
Remove structures menu will appear.
•
To select an image, highlight the image in the image
container and press the
Select
button. This will be
your Input image.
As an output image an image with the selected average
subtracted is computed and the result presented in the
Preview
window.
•
If the
Apply
button is pressed, the averaged
subtracted image stack will be opened as a new
image in the container.
You have four options that can be selected via the
Remove Structures drop down menu (Fig. 243):
None
,
Slowly moving structure
,
Immobile structures (+Stack)
and
Immobile structures (+Plane).
If None is selected, no average will be subtracted and the original image is kept. If Slowly moving
structure
is activated the
Average frames
input box becomes available. Type in the required number
(minimum is 2) or use the slider or arrows for input. The number defines the number of frames that will
be averaged and subtracted in a gliding way from the original stack in the following way:
•
From a stack of n frames take successive m moving average frames with an overlap of m-1 and
average these. The outcome is a new stack with n-m+1 gliding or moving average frames. Calculate
from each of the average frames the overall average of all pixels, which is a scalar.
•
Subtract the i-th of the gliding average frame from the (i-1)+m/2 original frame and add the i-th
scalar. In this way, the first frame to be used from the original stack is m/2 and the last m/2+(n-m+1).
This creates a new stack of n-m-1 frames that is the output image.
If
Immobile structures (+Stack)
is selected, the average frame of the stack will be computed and
subtracted from each original frame. This creates a new average subtracted stack of the same size. An
average value of all pixels from all frames is computed, which is a scalar, and added to each pixel of the
single frames of the average subtracted stack to avoid negative numbers. The resulting stack is the
output image.
If
Immobile structures (+Plane) is selected, the average frame of the stack will be computed and
subtracted from each original frame. This creates a new average subtracted stack of the same size.
Average values of all pixels from each of the original frames is computed, which is a scalar, and added to
each pixel of each corresponding single frame of the average subtracted stack to avoid negative
numbers. The resulting stack is the output image.
Fig. 243 Remove structure drop down
menu