Image Section Generator Documentation

Author and Maintainer: Alison Chaiken
650-279-5600

Overview

Linescans generated by Image Section Generator plotted together after export.

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 above.

Inspiration

The original inspiration for ISG comes from the Section Analysis mode 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

File Selection dialog

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:
- 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.
- 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 cursor")
  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.

Other features:

Color 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

Installation

Image Section Generator was created using Mathworks' wonderful Matlab R2009a package. The current version isn't as bomb-proof or featureful as I'd like yet. If you're looking at a local copy of the documentation, be sure to check the latest version on the website. The source code is released under the terms of the Gnu Public License version 3. Image Section Generator is free, both as in free beer and as in freedom.

Running from source files using your existing Matlab installation (Linux, Solaris, Mac or Windows)

(tested on Fedora 8 and Windows XP)

Download the source tarball or Zip archive and unpack:

  mkdir ISG
  mv ImageSectionGeneratorSource.tar.gz ISG
  cd ISG
  tar xfz ImageSectionGeneratorSource.tar.gz

Start Matlab and then start GUIDE by typing "guide" at the command window >> prompt.
In the GUIDE Quick Start window that opens, select the "Open Existing GUI" tab. Click on ImageSectionGenerator.fig and then push the "Open" button.
An *editable* GUI opens. You don't want to edit the GUI, though; just type Ctrl-T at this window to run it.
Image Section Generator will start in its own window. Follow the "How to Use ISG" instructions below.

Running the stand-alone binary independent of Matlab (Linux x86 only)

(tested only on Fedora 8)

Download the executable tarball and unpack the archive:
```
  mkdir ISG
  mv ImageSectionGeneratorExecutable.tar.gz ISG
  cd ISG
  tar xfz ImageSectionGeneratorExecutable.tar.gz
```
The tarball is large (currently 207 MB) because it includes the Java Virtual Machine (JVM) you will need to run the program. (Obviously I didn't create the JVM; I got it from Mathworks, who got it from Sun. Sun's license terms apply.)
Run the MCRInstaller.bin program to install the JVM:
```
./MCRInstaller.bin
```
Answer all questions about where you want the JVM and let the installation complete. A directory called MATLAB_Compiler_Runtime will be created.
Invoke the executable as
```
./run_ImageSectionGenerator.sh $HOME/MATLAB_Compiler_Runtime/v710
```
assuming that the directory MATLAB_Compiler_Runtime is in your home directory. (If not, fix the path name.)
A running Image Section Generator window should open. Operate the application as specified in "How to Use ISG" above.

Running the stand-alone binary independent of Matlab (Windows only)

(tested only on Windows XP)

Download the executable zip archive and unpack into a new folder. The zip archive is large (currently 299 MB) because it includes the Java Virtual Machine (JVM) you will need to run the program. (Obviously I didn't create the JVM; I got it from Mathworks, who got it from Sun. Sun's license terms apply.)
Run the program MCInstaller.exe from the DOS shell prompt. The MCR is the MATLAB Compiler Runtime, which is essentially the JVM.
Follow Mathworks' instructions in section 4A of the file readme.txt to properly set the PATH environment variable so that Windows finds the MCR.
Now invoking ImageSectionGenerator_pkg.exe should start Image Section Generator.
A running Image Section Generator window should open. Operate the application as specified in "How to Use ISG" above.

Features to be added

Movable markers on the section, as in the Veeco AFM software.
Optional display of image metadata and output to file.
Easy, automated scale calibration method.

Known Bugs

In Windows, the placement of windows on the screen is poor. I have not tested the Linux version on a variety of screen sizes, and there may be problems there as well.

If you see other bugs or have other suggestions for improvement, please email me.