Image Analysis Program
Macros Used in Scion Image
- Macros for building STEREO files
- Macros used to build STEREO data file, Should work with the interface program Build_f.exe. Macros in this set include: Reset for Quantitative Stereology, Find Tissue, Get Tissue Area, Outline Data, Find Focal Transections, Highlight focal transection, Edit focal transection, Get Focal Trans. Data, Locate Anatomic Marker A, B, Draw 1 cm Scale on Photo, Set Density Slice at..., Make Tissue Plot, etc.
- Macros for obtaining nuclear data
- Macros used to count nuclei automatically, Should work with the interface program Brdu.exe. Macros in this set include: Reset for Nuclei Counting...,Find nuclei , Green Highlight Nuclei, Get Nuclei Data, etc.
Microsoft .NET Framework
Microsoft .NET Framework Version 1.1 Redistributable Package.
Program
Following programs are developed in this laboratory using Microsoft Visual Basic 6.0 Professional version. An IBM-compatible PC with high speed CPU and large memory is needed. In this lab, we use a PC with Pentium microprocessor 450 and 126 MB RAM running Windows XP with service pack 2 ( Windows 95/98 OK ) operating system and MS Office . To run these programs on your computer, you should install Microsoft VB6.0 run time files first. These programs are designed to 1024 x 768 screen resolution so please set the display resolution at 1024 x 768
- VB6.0 Run_time files, 2.9 mb
- A set of programs that are necessary to run VB6.0 application. Unzip it in a temporary folder and install it. ( by clicking Setup.exe ) you can install them into any folder you want.
- Stereo1.zip, 1803 kb
- 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. This set of programs has the basic function only ( light version ). To run it correctly, you should unzip this ZIP file into C:\VBSTEREO directory. Note: The directory name can not be changed! This software package is designed to 1024 x 768 screen resolution. Please set the display resolution at 1024 x 768. The best size of the tissue image is 640 x 480 pixels.
- Build_f.zip, 41 kb.
- This zip file includes two interface programs used to build STEREO data file by using Scion Image, They should work with STEREO program and Macros for building STEREO files. They are already included in Stereo1.zip file.
- Nu_count.zip , 26 kb
- This zip file includes an interface program Brdu_a.exe used to count nuclei automatically using Scion Image, It should work with Macros for obtaining nuclear data. To run it correctly, You should install Stereo1.zip file first, then unzip this file into C:\VBSTEREO directory.
- NLIA.zip, 389 kb
- This zip file includes a software package NLIA ( Nuclear Labeling Index Analysis) which is used to perform accurate and automatic nuclear labeling index analysis . It consists of: NLIA.exe, and Image_nu.txt (macros text file). you should install Microsoft VB6.0 run time files first and then install this software package This software package is designed to 1024 x 768 screen resolution. Please set the display resolution at 1024 x 768. The best size of the image for nuclei counting is 640 x 480.
3D Estimation, 2.5M
- 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. After entering the 2D focal transection data, the user can obtain 3D estimation results (total number of foci in liver and detailed information about foci size distribution) by a single click on the “3D Convert” button. This software is designed to 1024 x 768 screen resolution. Please set the display resolution at 1024 x 768. To get this software, one should Send request to Dr. Pitot. Please included the name, address, title, institution, the software name needed in the email. The E-mail address given should have the capacity to hold the attached software.
- 3D Viewer, 7.8M
- This zip file includes a software 3D Viewer which 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. In 3D_Viewer, each of these functions forms a sub program. This software is designed to 1024 x 768 screen resolution. Please set the display resolution at 1024 x 768. To get this software, one should Send request to Dr. Pitot. Please included the name, address, title, institution, the software name needed in the email. The E-mail address given should have the capacity to hold the attached software.
This zip file includes a software CpG Analyzer which 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. This software is designed to 1024 x 768 screen resolution. Please set the display resolution at 1024 x 768. To get this software, one should Send request to Dr. Pitot. Please included the name, address, title, institution, the name of the software needed in the email. The E-mail address given should have the capacity to hold the attached software.