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@med.rug.nl> Subject: [BioC] Blurriness assesment of scanner TIFF files To: "Bioconductor" <bioconductor@stat.math.ethz.ch> Message-ID: <002801c3dea2$59154420$a38f7d81@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 [[alternative HTML version deleted]]