SOFTWARE FOR IMAGE SEGMENTATION AND ANALYSIS
IN PATHOLOGY (ISAP).
WELCOME TO ISAP.
Copyright © 1994 G. William Moore, Geoffrey W. Moore,
Jules J. Berman, Lawrence A. Brown.
http://www.medparse.com/isapwlcm.htm
U. S. Government Work, presented at the 1994 meeting
of the American Society of Clinical Pathology, Washington, DC.
Moore GW, Berman JJ, Moore GW, Brown LA.
Software for Image Segmentation and Analysis in Pathology (ISAP)
Am J Clin Pathol 102:538-539, 1994.
IMAGE SEGMENTATION AND ANALYSIS IN PATHOLOGY (ISAP).
INTRODUCTION.
Welcome to IMAGE SEGMENTATION AND ANALYSIS IN PATHOLOGY (ISAP),
written by Drs. Berman, Brown, Moore, and Mr. Moore.
Attached herewith are four abstracts [1,2,3,4]
of possible interest to the reader.
The program is written in MICROSOFT(R) VISUAL BASIC. The most innovative
part of this software is the nuclear border thresholding method,
which involves creating a histogram of pixel densities in an area
including the nucleus and surrounding cytoplasm. The software
then dissects the histogram into high-density and low-density segments,
using a least-squares method [3]. A demonstration program
and Perl source code to perform this procedure are given at URL:
http://www.medparse.com/isapver2.htm
We recommend that you refer to Dr. Berman's excellent tutorial,
entitled PERL FOR PATHOLOGISTS [5].
The executable files and other necessary files for the software will be
emailed upon request as attachments. Send queries to the administrator
of The Johns Hopkins Autopsy Resource (JHAR) at:
.
webmaster@netautopsy.org .
The programs have been tested successfully on Microsoft(R) Windows 95,
Windows 98, and Windows NT. In order to run this software,
you must also have a copy of the file VBRUN300.DLL, a copyrighted
Microsoft(R) file.
Please load all the files into a directory named ISAP, and verify
that they are all present in your directory (see below).
Then click on START, click on RUN, enter C:\ISAP\ISAP.EXE,
and click OK. The ISAP license agreement appears. Click OK.
The DATABASE query appears. Click OK. Click FILE. Click OPEN IMAGE.
Click ISAP.BMP. Click OK. Click on IMAGE, and click on BLOCK SELECT.
Follow the instructions. Click OK. Trace the image while dragging
the left-mouse button. Release the left-mouse button.
Image statistics will appear.
REFERENCES.
1.
Berman JJ, Moore GW, Brown LA.
ISAP v.2: Software for image segmentation and analysis in pathology.
http://www.netautopsy.org/isaptwoo.htm
ISAP, version 2, is an image display and analysis software application
developed at the Baltimore Veterans Affairs Medical Center and available at
no cost to pathologists, including executable file and source code in
Microsoft(R) Visual Basic. Users interactively surround cells of interest
using a mouse. In version 2, ISAP permits a choice of methods for smoothing,
thresholding, and edge detection. ISAP thresholds the enclosed image, either
manually by preselecting a grayvalue threshold or percentage threshold, or
automatically according to an algorithm published previously by the authors.
ISAP quantitates nuclear features, including measurements of nuclear size
(area, summed optical densities, greatest diameter, least diameter); nuclear
rim shape (ratio of greatest-to-least diameter, perimeter, contour, fractal
dimension); and chromatin texture (standard deviation of optical density,
histogram of optical densities). Cytologic measurements are saved in an
external database that can be uploaded into commercially available
spreadsheet applications for statistical analysis of cell populations.
ISAP uses Targa or Windows (.BMP) image formats, and operates
on IBM-compatible computers with at least 5 MB hard drive memory,
Microsoft(R) Windows v. 3.0 or higher, and 256-color display.
To test the robustness of ISAP algorithms, we performed image analysis on
20 normal intermediate cell nuclei at 40x magnification from
Papanicolaou-stained cytology smears of the uterine cervix and vagina.
Each cell-image was captured as a black-and-white image on a grid of 756 x 486 pixels, with
256 gray-levels per pixel. For each cell, we obtained 10 measurements in
focus, and 10 measurements apiece with the stage lowered by 0.1 mmm from the in-focus position, for a total of 400 image-analyses. Area and perimeter were compared by one-way analysis of variance, and were not statistically different in the two focal planes. Results suggest that ISAP is a robust image analysis application, which permits repeatable descriptors for nuclear area and shape in cytologic image analysis.
2.
Moore GW, Berman JJ, Sydnor DL.
Fractal dimension for pathology images,
a repeatable and quantitative measurement
of nuclear rim irregularity.
Am J Clin Pathol 102:538, 1994.
http://www.netautopsy.org/ascpfrac.htm
3.
Moore GW, Berman JJ, Moore GW, Brown LA.
Software for image segmentation and analysis in pathology (ISAP):
public domain image software and source code developed at the Baltimore
VA Medical Center.
Am J Clin Pathol 102:538-539, 1994.
http://www.netautopsy.org/ascpisap.htm
4.
Moore GW, Berman JJ, Sydnor DL.
Automated edge detection in image analysis:
distinguishing the nucleus from the
cytoplasm without a user's threshold estimate.
Am J Clin Pathol 102:539, 1994.
http://www.netautopsy.org/ascpedge.htm
5.
Berman JJ.
http://www.pathinfo.com
Scroll to the bottom of the page,
and click on PERL FOR PATHOLOGISTS.
IMAGE SEGMENTATION AND ANALYSIS
IN PATHOLOGY (ISAP),
DIRECTORY.
ISAP EXE 90,580 09-18-94 9:55p ISAP.EXE
ISAP BMP 362,939 07-26-93 3:59p ISAP.BMP
ISAP FRM 78,348 09-18-94 8:23p ISAP.FRM
ISAP ICO 4,158 07-22-93 4:34p ISAP.ICO
ISAP LIC 1,284 04-28-94 7:35a ISAP.LIC
ISAP MAK 104 09-18-94 8:23p ISAP.MAK
ISAP TXT 69,803 09-18-94 8:23p ISAP.TXT
ISAPANLY TXT 2,997 08-22-94 9:33a ISAPANLY.TXT
ISAPBLKS TXT 529 09-03-94 3:58p ISAPBLKS.TXT
ISAPCOPR TXT 1,266 08-22-94 9:30a ISAPCOPR.TXT
ISAPDTBS TXT 1,096 08-22-94 9:21a ISAPDTBS.TXT
ISAPEDGE TXT 1,752 08-22-94 9:22a ISAPEDGE.TXT
ISAPFILE TXT 1,453 08-22-94 9:22a ISAPFILE.TXT
ISAPGNRL TXT 993 08-22-94 9:30a ISAPGNRL.TXT
ISAPHEAD TXT 753 08-22-94 9:18a ISAPHEAD.TXT
ISAPHELP TXT 1,044 08-22-94 9:31a ISAPHELP.TXT
ISAPHIST TXT 618 08-22-94 9:22a ISAPHIST.TXT
ISAPIMAG TXT 1,219 08-22-94 9:32a ISAPIMAG.TXT
ISAPPALE TXT 801 08-22-94 9:42a ISAPPALE.TXT
ISAPPRIM TXT 559 08-22-94 9:32a ISAPPRIM.TXT
ISAPPROG TXT 3,300 09-04-94 8:04p ISAPPROG.TXT
ISAPSRCH TXT 17,666 09-18-94 8:37p ISAPSRCH.TXT
ISAPTHRS TXT 433 08-22-94 9:18a ISAPTHRS.TXT
ISAPTRUB TXT 1,939 08-22-94 9:21a ISAPTRUB.TXT
ISAPVALU TXT 2,453 08-22-94 9:21a ISAPVALU.TXT
48GRYFL1 HDR 1,095 06-25-93 2:33p 48GRYFL1.HDR
48GRYFL2 HDR 1,095 06-25-93 2:41p 48GRYFL2.HDR
BLUE HDR 1,095 06-28-93 1:27p BLUE.HDR
DATABASE HDR 255 07-19-93 10:46p DATABASE.HDR
EXTREME HDR 1,080 06-18-93 1:40p EXTREME.HDR
EXTREME2 HDR 1,080 06-30-93 4:03p EXTREME2.HDR
GREEN HDR 1,080 06-28-93 1:27p GREEN.HDR
GREY HDR 1,095 06-18-93 1:02p GREY.HDR
GREYFLPS HDR 1,080 07-07-93 3:01p GREYFLPS.HDR
GRY16 HDR 1,080 07-07-93 2:58p GRY16.HDR
GRYFL1 HDR 1,080 06-29-93 1:54p GRYFL1.HDR
GRYFL2 HDR 1,080 06-29-93 1:52p GRYFL2.HDR
GRYFL3 HDR 1,080 07-02-93 3:50p GRYFL3.HDR
GRYFL4 HDR 1,080 06-29-93 1:45p GRYFL4.HDR
GRYFL5 HDR 1,080 06-29-93 1:40p GRYFL5.HDR
GRYFL6 HDR 1,080 06-29-93 1:36p GRYFL6.HDR
INVER1 HDR 1,082 07-02-93 4:41p INVER1.HDR
INVER2 HDR 1,082 07-02-93 4:41p INVER2.HDR
INVER3 HDR 1,082 07-02-93 4:41p INVER3.HDR
INVER4 HDR 1,082 07-02-93 4:41p INVER4.HDR
INVER5 HDR 1,082 07-02-93 4:41p INVER5.HDR
INVER6 HDR 1,082 07-02-93 4:41p INVER6.HDR
MUL HDR 1,080 07-07-93 3:46p MUL.HDR
RAINBOW HDR 1,095 06-18-93 1:46p RAINBOW.HDR
RED HDR 1,095 06-28-93 1:27p RED.HDR
SPRINKLE HDR 1,080 06-18-93 1:34p SPRINKLE.HDR
IMAGE SEGMENTATION AND ANALYSIS
IN PATHOLOGY (ISAP),
INTERNET URLs.
http://www.medparse.com/isap/isap.exe
http://www.medparse.com/isap/isap.bmp
http://www.medparse.com/isap/isap.frm
http://www.medparse.com/isap/isap.ico
http://www.medparse.com/isap/isap.lic
http://www.medparse.com/isap/isap.mak
http://www.medparse.com/isap/isap.txt
http://www.medparse.com/isap/isapanly.txt
http://www.medparse.com/isap/isapblks.txt
http://www.medparse.com/isap/isapcopr.txt
http://www.medparse.com/isap/isapdtbs.txt
http://www.medparse.com/isap/isapedge.txt
http://www.medparse.com/isap/isapfile.txt
http://www.medparse.com/isap/isapgnrl.txt
http://www.medparse.com/isap/isaphead.txt
http://www.medparse.com/isap/isaphelp.txt
http://www.medparse.com/isap/isaphist.txt
http://www.medparse.com/isap/isapimag.txt
http://www.medparse.com/isap/isappale.txt
http://www.medparse.com/isap/isapprim.txt
http://www.medparse.com/isap/isapprog.txt
http://www.medparse.com/isap/isapsrch.txt
http://www.medparse.com/isap/isapthrs.txt
http://www.medparse.com/isap/isaptrub.txt
http://www.medparse.com/isap/isapvalu.txt
http://www.medparse.com/isap/48gryfl1.hdr
http://www.medparse.com/isap/48gryfl2.hdr
http://www.medparse.com/isap/blue.hdr
http://www.medparse.com/isap/database.hdr
http://www.medparse.com/isap/extreme.hdr
http://www.medparse.com/isap/extreme2.hdr
http://www.medparse.com/isap/green.hdr
http://www.medparse.com/isap/grey.hdr
http://www.medparse.com/isap/greyflps.hdr
http://www.medparse.com/isap/gry16.hdr
http://www.medparse.com/isap/gryfl1.hdr
http://www.medparse.com/isap/gryfl2.hdr
http://www.medparse.com/isap/gryfl3.hdr
http://www.medparse.com/isap/gryfl4.hdr
http://www.medparse.com/isap/gryfl5.hdr
http://www.medparse.com/isap/gryfl6.hdr
http://www.medparse.com/isap/inver1.hdr
http://www.medparse.com/isap/inver2.hdr
http://www.medparse.com/isap/inver3.hdr
http://www.medparse.com/isap/inver4.hdr
http://www.medparse.com/isap/inver5.hdr
http://www.medparse.com/isap/inver6.hdr
http://www.medparse.com/isap/mul.hdr
http://www.medparse.com/isap/rainbow.hdr
http://www.medparse.com/isap/red.hdr
http://www.medparse.com/isap/sprinkle.hdr
http://www.medparse.com/isapwlcm.htm
http://www.medparse.com/isapedge.htm
http://www.medparse.com/isaphist.htm
http://www.medparse.com/isapvalu.htm
http://www.medparse.com/isaptrub.htm
http://www.medparse.com/isapsour.htm
http://www.medparse.com/isapform.htm
http://www.medparse.com/isapver2.htm
For additional information, send queries to the administrator
of The Johns Hopkins Autopsy Resource (JHAR) at:
.
webmaster@netautopsy.org .
Last Updated: January 26, 2003, by G. William Moore, MD, PhD.