[BioC] Re: Blurriness assesment of scanner TIFF files

[Simon Lin]

Hi, Edo:

I would like to share some opinions slightly outside of the image analysis
context.

To calibrate the scanner, it is better to use some calibration slides. There
should be some 'standard patterns' on this calibration slide. Like the 'test
paper' used by the Xerox copier repairman with lines and meshes at different
intervals, or the checker board pattern used by the TV repairman.

To make this calibration slide, a high-end solution is photo-etching. A
quick solution is to spot some fluorescent dyes at known positions.

Even for people with no obvious problem of the scanner, this should be
checked at a regular interval to ensure the operating condition of the
scanner. Ask the scanner maker; they may do the service.

An accurate physical measurement will solve many of our headaches down the
road!

Good luck!

Simon

=================================================
  Simon M. Lin, M.D.
  Manager, Duke Bioinformatics Shared Resource
  Assistant Research Professor, Biostatistics and Bioinformatics
  Box 3958, Duke University Medical Center
  Durham, NC 27710
  Ph: (919) 681-9646 FAX: (919) 681-8028
  Lin00025 (at) mc.duke.edu
  http://dbsr.duke.edu
=================================================

Message: 3
Date: Mon, 19 Jan 2004 16:38:55 +0100
From: "Edo Plantinga" <A.E.D.Plantinga at med.rug.nl>
Subject: [BioC] Blurriness assesment of scanner TIFF files
To: "Bioconductor" <bioconductor at stat.math.ethz.ch>
Message-ID: <002801c3dea2$59154420$a38f7d81 at edo>
Content-Type: text/plain

Dear all,

At our department we have experienced some difficulties with our microarray
scanner. I am looking for some software that can read in the raw TIFF files
that come out of our scanner to asses how blurry the picture is (i.e. how
sharp the edges are in the picture). I would also like to know which areas
of the picture are the most blurry (we suspect a left to right effect). Does
anyone know of (R?) software that can do this?

Kind regards,

Edo Plantinga
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