Sushmita Thakare BBT-1-06015

Micro Measure 

Overview

Since MM is intended specifically for linear chromosome measurement (unlike other image analysis programs), characteristics commonly used by chromosome cytologists (such as centromeres, bands, fluorescent foci, etc.) may be easily marked, and standard data types (e.g. relative lengths of chromosomes or chromosome arm ratios) are computed automatically in an Excel spreadsheet.

Users may also customize the traits to be marked with MM, and using the flexible data spreadsheet, conduct more specialized analyses.

This software package is made available to researchers without cost by the Biology Department at Colorado State University. Please see the copyright notice and terms of use for more information.

Features

Several features contribute to the ease of using MM:

• Measurement of chromosomes and marking of associated characteristics are carried out rapidly and accurately with a mouse or other similar pointing device

• Measurement options may be customized to meet the requirements of a wide variety of research projects

• Many commonly used calculations are computed automatically

• Automatic transfer of user-selected data to Microsoft Excel allows for more complex analysis

• Data reports may be generated or altered at any time, without repeating initial analyses

• Image tracings may be hidden, allowing simplified analysis of complex images

• Text may be added to images to allow for on-screen annotation

• Comments may be entered and automatically associated with individual images using Microsoft WordPad

System Requirements

• Microsoft Windows 95, 98, 2000, Millenium Edition, or NT 4.0

• Mouse or compatible pointing device

• Microsoft Excel version 5.0 or higher

• Display capable of at least 256-color output at a resolution of 800 x 600 pixels

• Microsoft WordPad (included with Windows) must be installed to use selected features.

• An Internet browser is required for access to program documentation and help

  Minimum: Netscape Navigator 3.0 or compatible

  Recommended: Microsoft Internet Explorer 4.0 or higher    

  Each MicroMeasure project includes all of the data, calculations, and notes usually associated with a set of chromosomes in an image. Since a digitized image provides the basis for a MM project, the first step in creating a project is selecting the image file to use. Digitized images from any source (scanned micrographs or negatives, electronically captured images, etc.) are suitable for analysis with MM.

  MM will prompt the user to select an image file when the Create New Project... command is selected.

  Initial Settings

   After an image file is chosen, the user is prompted to make two initial settings. The project name is used to identify all data sets generated from this project. By default, the file name of the image is used as the set ID.

  The second setting is the image magnification, on which all calculations are based. This value will usually be the magnification at which the original image was taken. If, however, any additional enlargement or reduction took place at any time,the user must account for this for absolute measurements to be accurate. See How Calculations Are Made for more information about this topic.

  While this is a convenient time to make these two initial settings, neither is required until the user wishes to calculate measurements. These settings may be entered or changed at any time using the Set | Initial Settings... command.

  Once an image file has been selected, the user can begin marking chromosomesMarking Chromosomes

  With MicroMeasure, users create a tracing of the chromosomes or other features present in an image. From this tracing, measurements may then be calculated. Each tracing is made up of a series of connected line segments marked in the MM window.

  The figure below illustrates how a chromosome with a centromere is marked. Click on the Forward or Back arrows to view each step.

  Data Tabs

  There are several tabs in the Data window, each of which shows the types of measurements that can be produced by MM. The Lengths tab, for example, lists characteristics of chromosomes, such as total length, relative length, and arm ratio. By selecting from the available options, the user chooses which parameters to calculate and export to a spreadsheet. After making a selection, the user can click the OK button to produce a report.

  Two Data tabs are always shown: the Lengths tab (mentioned above), and the Eu- and Heterochromatin tab. If a user has defined custom point or segment types, an additional tab will appear for each custom type.

  The sample Data window above shows a total of 4 tabs, including the two default tabs, one for a custom point type (simply called Point in this example), and one for a custom segment type (Segment). To view the different calculations or measurements possible on each tab, select one of the four tabs. Click on the various calculation types to see a longer description of the calculation and how each is produced.