Computer Programming
Our laboratory has developed several computer programs using Microsoft Visual Basic programming language. The platform for these programs is PC-Windows. To see the detail information, go to the download site
- STEREO
- A set of programs to get 3 dimensional data from the observation of a random cut 2 dimension slide of the sample. Sample used in this laboratory is the rat liver during chemical carcinogenesis. [Paper Abstract]
- NLIA
- NLIA ( Nuclear Labeling Index Analysis) is used to perform accurate and automatic nuclear labeling index analysis. This application software is designed to work cooperatively with Scion Image, a free image analysis software from Scion Corporation. This software package consists of: NLIA.exe, and Image_nu.txt (macros text file). [Paper Abstract]
- 3D Viewer
- 3D Viewer is used to do 3D reconstruction from the digital images taken from the serial sections. This application software was designed to work cooperatively with Adobe Photoshop, a commercial graphic software. 3D Viewer supplies four basic functions that are essential for 3D reconstruction, while the other graphic functions can be found in Adobe Photoshop. These four functions are: a) image aligning, b) movie-frame-image generation, c) movie viewing, and d) shift-overlay image generation. Among these functions, the movie-frame-image generation and movie viewing are the most important. [Paper Abstract]
- 3D Estimation
- 3D_estimation.exe was developed in this laboratory on the basis of an improved stereologic method for three-dimensional estimation of particle size distribution from observations in two dimensions (25 association factors method). It can be used to estimate the number of altered hepatic foci in rodent liver on a three-dimensional basis. [ Paper Abstract]
CpG Analyzer is a utility program for DNA methylation studies. The bisulfite genomic sequencing technique has found wide acceptance for determination of the DNA-methylation status down to a level of nucleotide resolution. Knowledge of the CpG dinucleonal distribution in the DNA sequence to be studied, highlighting each CpG inside the sequence, and converting the test sequence into bisulfite-modified (methylated and un-methylated) sequences are essential to this technique. This program 1) searches and records CpG locations and displays the CpG location data in graphic plot and tabled number values, 2) generates modified DNA sequences that will result after bisulfite treatment, which can be used in bisulfite sequencing PCR assay and DNA methylation mapping, and 3) highlights CpGs in sequence text and keeps the GenBank flat file format unchanged. CpG Analyzer is designed to operate with Microsoft Office suite cooperatively. The graphic and tabled number data of CpG distribution information, the converted bisulfite-modified strands, and the CpG highlighted text can be exported into MS Office.
Image_Better
Image_Better consists of two sub application programs (BK_Correction and Pixel_Separator) which are used in our stereology system. With BK_Correction, common background problems such as incorrect color temperature setting, color shading and uneven light illumination background, can be corrected. With Pixel_Separator different types of objects can be separated from each other in relation to their color, such as seen with different colors in immunohistochemically stained slides. The resultant images of such objects separated from other components are then ready for particle analysis. Objects that have the same darkness but different colors can be accurately differentiated in a grayscale image analysis system after application of these programs.
