33
DP Data Processing Software Version 4.2
38
4.1.2 Points
The Points tool can be used to measure the
channel value at a point. In this case, the image is
height, so the height information is read out at the
position where the points cursor is set.
The coordinates are given in pixels (I,j), and as
lengths – within the image, and relative to the
overall (x,y) coordinates of the scan piezo.
4.1.3 Section
The Section tool opens a cross-section panel for
measuring the range of image values along a line.
The line is set by clicking and dragging in the image
panel. The coordinates can also be entered or ad-
justed by hand, so the same sections can be made
through several images.
The range of values along the line is given in the
Cross section control panel tab. The length of the
line can be shown in the image using Show length
on line.
Images exported from the main image panel will
show the section line, and also the length value if
selected. The cross-section is updated dynamically
as operations are applied to the image.
If the mouse is used to click and drag in the cross-
section panel rather than the image panel, then
markers are shown on the line section. The point-to-
point measurement is also shown in the control
panel. This can be used to measure the separation
or height difference between features. In this case
the periodicity of the collagen fibrils is measured as
67 nm.
25
DP Data Processing Software Version 4.2
39
Using the mouse to right-click in the cross-section
panel shows a menu for exporting the cross-section
information. Save data exports the ASCII values as
a file. Save image exports a TIFF image of the
current cross-section view. This menu can also be
used to change the view to other analysis tools, such
as Histogram or FFT (Fourier Analysis).
4.1.4 Histogram
The Histogram tool plots a histogram of the channel
values.
Here, for instance, the large peak around 0 nm
height value is due to the glass background, where
all the heights are within a narrow range. There are
two broad peaks, one around 50 nm and a second
around 150 nm, corresponding to the nuclear debris
and the chromosomes, respectively.
(Note – the color scale is also shown on the histo-
gram panel, this can help with setting the View pa-
rameters, see Section 2.3.2)
When a region is selected in the image panel, the histogram is only calculated using the pixels in the selected area. In the
left hand screenclip, an area of the mica is selected, and the histogram shows only values around 0 nm. In the right hand
screenclip, an area corresponding to chromosomes sitting on nuclear debris has been selected, and the two broader
peaks are now clearly distinguished.
Online Remove password from protected PDF fileOnline Remove Password from Protected PDF file. Download Free Trial. Remove password from protected PDF file. Find your password-protected PDF and upload it.
convert protected pdf to word online; create password protected pdf reader
24
DP Data Processing Software Version 4.2
40
The height can be measured by clicking in the histogram
panel and the value is shown in the control panel.
Sometimes a high number of pixels from one height level
obscures smaller peaks. This may be the case with ob-
jects against a flat background, or as here where some
lipid layers show more area than others.
In these cases, displaying the log of the frequency values
as shown here allows the smaller peaks to be better dis-
tinguished.
Histograms can be saved using the right mouse button
menu – either as ASCII data or as a TIFF image.
4.1.5 FFT
The FFT tool opens the Fourier Analysis panel, which
shows the image information as spatial frequencies
(i.e. 1/length). The center of the FFT panel corres-
ponds to the smallest spatial frequencies (largest dis-
tances measured in the image). The edges of the FFT
panel correspond to the largest spatial frequencies
(smallest distances in the image).
The display options for the FFT panel are shown at the
bottom, these require careful setting, since the range
of values is so high.
18
DP Data Processing Software Version 4.2
41
The right-click menu shows various options for the
view, including an option to change the colortable (for
the FFT panel only, this does not affect the real-space
image display). The FFT view can also be exported as
a TIFF file using Export Image.
4.2 Crop
The Crop tool can be used to select an area to form a new image file. In the example below, one
group of micelles is selected on the left hand side, and the cropped image is shown on the right hand
side. The new image has the same number of pixels as were selected from the original image, and
can be rectangular or square. The coordinates in the Crop panel can be used to set specific regions
for cropping, for example to crop the same region from several different images.
4.3 3D View
In addition to the normal view of the images shown in the
processing windows, as here, the information can also be
displayed as a projection of the 3D information. The 3D
icon opens the 3D view window.
25
DP Data Processing Software Version 4.2
42
The Data panel in 3D view can be used to select a re-
duced range of data to show in the projection, or to
change the range of the color scale.
Generally the smaller surface features are highlighted by
viewing the 3D height projections, so often different color
scales or height ranges need to be used to give better
results in 3D. The colortable is taken from the image when
3D is opened, so to change the colortable, close 3D view,
change the image colortable and re-open the 3D window.
The Projection panel in 3D view can be used to set the
viewing angles, as well as the scale factor applied to the z-
axis.
In this example, the Height of z axis has been increased
compared with the previous view.
The image can be rotated using the sliders here in the
Rotate View section. Clicking and dragging in the image
panel with the mouse allows the view to be changed free-
hand.
If the control key is held down during the mouse move-
ment (Ctrl-click and drag), then the projected image is
shifted around relative to the view window.
The whole view window can be resized to change the
proportions of the view for exporting images.
17
DP Data Processing Software Version 4.2
43
If the shift key is held down during the mouse movement
(shift-click and drag), then the projected image is zoomed
in or out, changing the way it fills the 3D view window.
The tickbox Coordinates in the Projection panel can be
used to switch on or off the axis display on the image.
Box adds a rectangular box outline showing the data
range (without any numbers).
TIFF images can be exported by using the right-click
menu and choosing Export as picture.
When the image is finally exported, then the whole region
within the left hand panel here is exported as a TIFF. The
black surrounding region is converted to a white back-
ground, and the spacing around the projected image is
maintained. If the image is zoomed to show only part of
the data, then only this part is exported.
28
DP Data Processing Software Version 4.2
44
§ 5 Direct Overlay
For those systems that have the Direct Overlay feature installed in SPM, calibrated optical images can be imported
into the DP software. The calibration must always have been made in SPM during measurement, as this is the conver-
sion from camera pixels to AFM coordinates. Any image file can be opened, so long as it has the same geometric
relationship as the calibration file. The illumination (phase contrast, fluorescence etc) and image format (jpg, png, tiff
etc.) are not important.
5.1.1 Opening Optical images
To open a JPK SPM file, select File > Import Optical Im-
age from the pull down File menu. Alternatively, click on
the blue open file icon.
A dialog will open in which the Calibration file and Image
file are chosen. Multiple Image files can be opened with
the same Calibration file, so long as they have the same
geometrical relationship between camera and AFM posi-
tions.
The optical image will appear in its own individual window
(similar to the processing window for AFM image scans) as
well as in the Overview window.
There are no processing operations for the optical images,
as the DP program is specialized for AFM images. The
optical images can be modified beforehand in other suitable
software. All processing operations that change color, in-
tensity, etc. are completely compatible with the optical cali-
bration and will not cause any problems. Processing that
changes the image geometry (cropping, scaling etc.) should
not be applied, as this will invalidate the calibration.
Documents you may be interested
Documents you may be interested
