From: Bob Leif To: cyto-inbox Since FCS is an island unto itself and was not created as medical software, it needs to be replaced. The feasibility of my proposed replacement, CytometryML, was demonstrated in a poster at ISAC. You motivated me to try to import my XML file into Excel. It worked! However, the column headings include excess information which needs to be removed. The correct data is in the row beneath. Because of its size, the actual list data should be kept binary. However the structure of this binary array of records is much simpler than that of FCS. The abstract of the paper I am about to submit to Cytometry is as Follows: Background: Flow Cytometry Standard, FCS, was initially created out of a need for researchers to be able to employ third party and their own software to analyze, transmit, and store the data produced by flow cytometers and sorters. Because of the clinical success of flow cytometry, it is necessary to have a standard consistent with the requirements of medical regulatory agencies. Method: First, employ the existing Digital Imaging and Communications in Medicine (DICOM) Standard documents to extend the mapping of the existing Flow Cytometry Standard (FCS) to DICOM including a mapping of both flow cytometry and microscopic image list-mode data to the DICOM Waveform Information Object. Then, create an XML schema to express the DICOM analytical cytology text based data-types. Accomplish this software project in an open environment that is subject to continuous peer review. Results: The feasibility of expressing the data contained in FCS including list mode in DICOM has been demonstrated; and a preliminary mapping for list mode data in the form of XML Schema and documents has been completed. DICOM permits the creation of indices to individual cell subsets. DICOM and its coding schemes for other medical standards can be represented by XML schemas, which can be combined with other relevant XML applications, such as Mathematical Markup Language, MathML. -----Original Message----- From: ba cotleur [mailto:bunny@cotleur.com] Sent: Wednesday, May 29, 2002 10:12 AM To: cyto-inbox Subject: EXPORTING RAW FCS DATA I just had a researcher ask if FCS data ((raw)) can be exported into Excel or similiar programs. He's interested in analyzing cell-by-cell the fluorescence. (Not sure why.......) Anyone have any advice? -- Bunny Cotleur, M.S. Sr. Technologist Cleveland Clinic Foundation Neurosciences NC30 9500 Euclid Avenue Cleveland, OH 44195 cotleur@ccf.org (216) 444-1164 fax (216) 444-7197 cell (216)905-2582
This archive was generated by hypermail 2b29 : Sun Jan 05 2003 - 19:26:11 EST