dot blot imaging

Sebastian Bunka Sebastian.Bunka at vu-wien.ac.at
Thu Nov 26 10:47:30 EST 1998


Maggie Amsler <mamsler at uab.edu> wrote:
> I am trying to analyze results from nuclear run on assays which essentially
> measure transcription rates.  The pertinent step is hybridizing radiolabeled
> RNA with membrane bound DNA.  The end result is 6 strips each with 32 hot
> dots that are put on a sheet of 8x10 AR film for awhile.  When the film is
> developed I have 198 dots of varying intensity on the film-essentially 2 96
> well plates of results.  The film is then scanned and I have been trying to
> use NIH/Scion Image software to analyze the digitized dots.  the best I can
> figure so far is to use the gelblot macro- making each dot a 'lane' and
> plotting each dot as a curve.  It is very laborious!  Anyone know of more
> appropriate software or a more efficient way to do this??  Thanks in advance
> for any input
I use tnimage; I think it works fine for dot plots;
You'll get a couple of statistics and calculations like:
Densitometry results
No.  Area    Total signal  Spot Density  Total Bckgd Bkg.Density   Net
densi. Signal-Bkgd


1    1920    1086.6268     0.5977        326.2964    0.1699        0.4278
366.6005
2    1849    1022.9490     0.5830        287.3617    0.1554        0.4276
374.1335
3    2064    1023.7766     0.5266        228.6885    0.1108        0.4158
331.8378
4    2100    1022.0203     0.5105        262.8418    0.1252        0.3854
345.2978
5    1554    691.5465      0.4743        247.5142    0.1593        0.3150
218.6342
6    1190    306.8573      0.2800        57.4325     0.0483        0.2317
110.2857
7    1280    203.4348      0.1785        47.0422     0.0368        0.1418
76.1252
8    1254    110.6109      0.1016        25.3722     0.0202        0.0814
37.3432
9    960     56.6612       0.0683        21.4129     0.0223        0.0460
15.2866
10   945     52.8204       0.0609        34.1953     0.0362        0.0248
7.9449
(sorry for the line breaks)

However you'll need a SUN or Linux box.

Hope this helps
SWB


Begin3
Title:          TN-Image image analysis program
Version:        2.8.1a
Entered-date:   24NOV98
Description:    Scientific image viewing and analysis program. Create, edit,
                label, rotate, annotate, analyze, and color print images in
                numerous formats from 1-32 bits/pixel, including medical
                grayscale, 3D PET scan images, animated GIFs, and custom
                formats. Handles 512 images simultaneously in separate
windows
                or in a single large window. Performs filtering, format
                conversion, image algebra, measurement and calibration,
                2D-FFT, convolution and deconvolution, densitometry of rec-
                tangular or arbitrary-shaped areas, grain counting, pattern
                recognition. Automatic background subtraction using fuzzy
                k-means, peak area calculation, smart object detection, and
                other advanced functions. Pixel values can be viewed and
                edited in spreadsheet. Image editing features including
zoom,
                warp, gradient flood fill, movies, Bezier curves, chromakey,
                transparency, multiple fonts, subscripts, rotated text,
                arrows, sprayable math and filtering, and
graphically-editable
                colormaps.  Has scanner and camera interface. Camera
interface
                allows live image accumulation, dark current subtraction,
and
                post-processing. New image analysis features are easily
added
                with plugins. Has user-definable buttons and programmable
macr
                language. Includes tutorials, sample plugin code and manual.
Keywords:       image FFT densitometry scan deconvolution graphics filtering
                scanner camera grain counting
Author:         tjnelson at las1.ninds.nih.gov (Thomas J. Nelson)
Maintained-by:  tjnelson at las1.ninds.nih.gov (Thomas J. Nelson)
Primary-site:   las1.ninds.nih.gov/pub/unix
                1846394 tnimage-2.8.1a.irix.tar.gz
                2273014 tnimage-2.8.1a.linux.lesstif.tar.gz
                2722163 tnimage-2.8.1a.linux.static.tar.gz
                1756432 tnimage-2.8.1a.linux.tar.gz
                1292512 tnimage-2.8.1a.manual.dvi.tar.gz
                 736624 tnimage-2.8.1a.manual.ps.gz
                1744031 tnimage-2.8.1a.solaris.tar.gz
                1276191 tnimage-2.8.1a.src.tar.gz
                las1.ninds.nih.gov/pub/dos
                477423 tnimg216.zip
Alternate-site: sunsite.unc.edu/pub/Linux/X11/apps/graphics/misc
Original-site:  las1.ninds.nih.gov/pub/unix
Platforms:      Linux, SGI Irix, Solaris, ConvexOS, or MS-DOS. Requires
Motif
                1.2 or higher (except for Linux versions which require Motif
                2.0) and X11R5 or higher. Static versions do not require
Motif
Copying-policy: Freely distributable
End



-- 
Sebastian Bunka, Dr. med. vet
Inst. Med. Chemistry, Vet. University Vienna
Ph. +43-1-250 77 ext. 4208, Fax: ext. 4290
e-mail: Sebastian.Bunka at vu-wien.ac.at



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