May 14, 2009
Author and Maintainer: Alison Chaiken
generated by Image Section Generator plotted together after
The purpose of Image Section Generator is to facilitate the
comparison of image data from different kinds of scientific
instruments, primarily optical, electron and scanned-probe
microscopes. Input images must be in TIFF or JPEG format. Both color
and grayscale images are supported. Via an interactive GUI front-end,
users can designate lines of arbitrary length and orientation along
which intensity values (either RGB triplets or grayscale scalars) are
extracted and plotted. ISG can export tab-delimited data to a text
file for import into another plotting or analysis package. A
representative plot comparing 3 ISG-generated section lines (colors)
with an idealized mask profile (black) can be found in the figure
The original inspiration for ISG comes from
of Veeco's Atomic Force Microscope image analysis
software. ISG allows similarly designated sections from optical and
electron microscope images to be replotted with section data exported
from Veeco's software.
How to Use ISG
- Load an image file for analysis by clicking the "Load new image"
button in the upper left "File I/O" panel and selecting a TIFF or JPEG
file from the list.
- Still in the File I/O panel, enter the magnification which is
applicable for the image, for example, "30" for 30x.
- Optionally examine the image by clicking the "Display image"
button on the "Image controls" panel. A message at the upper left of
the image shows its size in pixels.
- Choose one of two section designation methods:
section selected numerically
- horizontal or vertical sections ("Row/column numeric input")
Select "Row/column numeric input" on the "Section selection method"
panel if the section line along which data is extracted should have a
horizontal or vertical orientation and cross the entire image. Click
"horizontal line" or "vertical line" to select orientation. Either
use one of the preset buttons to indicate the line position or type a
numeric value in the "Location" window. Any typed numeric values must
fall within the range of the image size. For example, a vertical
section on a 480x640 (rows x columns) image must have a numeric
location between 1 and 640.
oriented section drawn with cursor
- for sections of arbitrary orientation and length ("Draw line with cursor")
Select "Draw line with cursor" on the "Section selection method"
panel. The horizontal-vertical controls are irrelevant and disappear.
- Click the "Make section plot" button
- for horizontal and vertical sections ("Row/column numeric input")
The section plot now appears in its own window.
- for sections of arbitrary length and orientation ("Draw line with
The user is presented with the input image. Move the cross-hair
cursor to the first end-point of the section, depress the left mouse
button, then move to the second end-point and release it. The section
plot now appears in its own window.
- Optionally "Save section data" to tab-delimited columns using a
button on the File I/O menu, or extract a new section from the same
image, or load another file.
image forced to grayscale with scalebar display
Optionally color images can be analyzed as if they were grayscale by
using a checkbox on the File I/O panel. The "Analyze as grayscale
data" checkbox is visible only for color images.
A scale bar can be displayed on images by clicking a checkbox on the
"Image controls" panel. Unchecking this box does not redisplay the
current image but only affects new image windows.
Calibration of Image Section Generator
Optical microscope image of a precision scale with an ISG section-line
ISG-generated line section used for
calibration of scan lengths
ISG has been calibrated for the author's imaging systems by
capturing similar views of the same precision scale on all of them
and changing program constants to match. To calibrate your system,
take an image of an object of known dimension and adjust the
Image Section Generator Source Code
Image Section Generator was created using Mathworks'
R2009a package. You can download the source code tarball or zip
archive but you will need Matlab to run it. The current version
isn't as bomb-proof or featureful as I'd like, but soon I hope to be
posting a new version, along with a .exe executable.