![]() ![]() The surface area measurement of long rods is more accurate and the measurement of volume is accurate in general (error < 1%) with worst case performance in perfect small spheres of less than 5% underestimation. This may be improved in the next version. When it is only 30 pixels in diameter, this underestimation is about 9%. For example, a 100 pixel diameter sphere will have a 4.6% underestimation in surface area. The worst performance is with perfect spheres in that approximation is least accurate. Issuesīecause of resolution limit and the algorithm cannot approximate the surface area and volume measurements using thin slices under pixel resolution. The surface area and the total volume of the cell are approximated by aggregating the surface area and the volume of the cone frusta. The cell is then sliced vertically into thin slices (typically with one pixel width). No manual work is needed after the plug-in launches. Then a rotation matrix is calculated from this angle to rotate the image. In Pombe Measurer, the actual coordinates of the outline of the cell are used and Principle Component Analysis is performed to find the long axis of the cell. When processing rod-shaped cellular images, one time-consuming task is to rotate the long axis of the cell in the image plane to be horizontal. It is recommended that you work on a copy of your file. The annotation will be drawn directly onto the image. Select Analyze Microscope Measurement Tools Draw Annotation - Line. Once you have entered the pixel length, click OK. Draw a Straight Line along the feature you want to measure (the length is displayed in the Fiji status bar) 2. If you need to change the pixel length later on, restart ImageJ. Click Plug-in - Pombe Measurer and it will pop up to let you input the pixel length. The input of the plugin needs an area selection. Jama package: Jama-1.0.3.jar from NIST websiteĭraw the outline of the cell using polygon tools in ImageJ. Start or restart ImageJ if you had it open. If you do not have JAMA, download it from NIST JAMA website. Also make sure that you have JAMA package in the same plugins folder. Alternatively, download the source file to the plugins folder then compile and run. class file into the plugins folder of your ImageJ installation folder. This plugin works with ImageJ and it requires the JAMA package to carry out the matrix manipulation. This plug-in of ImageJ (NIH) measures the length, width, surface area, and the volume of a rod shaped cell or spherical spores given that the user draws the outline of the cell as an ROI. Author: Zhou Zhou zz2181 AT columbia DOT eduĪffiliation: Laboratory of Fred Chang at Columbia University ![]()
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