Software

Following is a description of the FIMD analysis software FIM_ANALYSIS written by David Knowles as a PostDoc in the laboratory of Mohandas Narla.


FIM_ANALYSIS, which has saved an enormous amount of time in the analysis of images, currently manages a data base of over 7000 images. It quickly allows image display, semi automated quantitative image analysis and graphical display of the analysis output. The software and underlying data base has been developed to allow new aspects of analysis to be added and automatically implemented on previously analyzed data sets. Thus, the software package allows full developmental flexibility. This has been an essential feature which has kept the software driven analysis up to date with the science.

FIM_ANALYSIS is written above the image development platform SCILIMAGE. SCILIMAGE runs under Solaris and is licensed to, and use with permission from, the Digital Microscopy and Imaging Group (DMIG). FIM_ANALYSIS is written in C, runs on the SUN Workstations curlcurl.lbl.gov & bondi.lbl.gov and is accessible to all users of those machines. Users will require only a basic knowledge of UNIX commands with an understanding of the FIMD experiment to use the software and will require a more extensive knowledge of UNIX, C programming, optics, image analysis techniques and SCILIMAGE to develop FIM_ANALYSIS.

The FIM_ANALYSIS source code is in the directory /home/curlcurl/davidk/scilimage/myadditions/knowles/src

To evoke the software a user runs the command
/home/curlcurl/davidk/scilimage/sos5/scilimage.

The GUI is a drop down menu which includes basic SCILIMAGE functions and a button labeled KNOWLES. Under this button is the FIMD analysis routine FIM_ANALYSIS.

The major sequence of these commands involves:
openfile - open a new data output file to store analysis results
open10 - open 10 sequential FIMD images for analysis
fim_analysis - find the fluorescent object (user intervention is allowed) (see the above image)
a4 - plot the density distribution for the current image and store the analysis results in the in the output data file
closefile - writes the analyzed data to disk.
plot - replot the density entrance and cap densities from any data file. (see image below)

The remaining subroutines in the KNOWLES drop down menu are evoked by FIM_ANALYSIS and are there for developmental purposes