Abstract: A sample nucleic acid sequence is compared against a database to find a matching sequence. In one embodiment, this comparison is accomplished with a table look-up approach that involves using sequences with collapsed homopolymer regions.

Abstract: A method for increasing the accuracy and the types of data measurements of laser scanned dye stained cells, in a single sample, by means of multiple assays, utilizing cell positions as a factor in merging data measurements. Change in lasers, use of different cell dye stains and different treating reagents provide additional data regarding cells of the sample and fixing of cell positions in the first assay permits merging of the data obtained in subsequent assays.

Abstract: A network system for review and analysis of computer encoded microscope slides and specimens which were originally computer encoded from a microscope (attached via an encoder device to a local computer site), during an initial examination. The encoding includes parameters of viewing locations and events of interest on the slide, with such information being stored on a networked file server. The encoding also includes information regarding the manner in which the initial examination was conducted, for quality control purposes. The computer encoded information is retrievable at all remote locations of the network (either local or connected via modem) for supervisor review or for pathologist analysis. The network is further constituted by microscope sites having similar computer encoding devices attached thereto, which function, in this aspect, as computer terminals of the network. For enhanced analysis, the computer terminals have direct access to patient background information, e.g.

Abstract: Cell samples, stained with a fluorescent dye, taken up by DNA in the individual cells, are scanned with a cytometer, which measures the integrated value of fluorescent light/cell. The integrated values of all of the cells are compiled to create an histogram of cell counts versus integrated fluorescent light, representing a cell population of (a) cells having a complement of DNA, but not in the process of division (G.sub.0 phase), (b) cells having two full compliments of DNA, but which have not actually divided into two cells (G.sub.2 phase) and (c) cells which are in the process of replicating their DNA (S, separation phase). The percentages of cells in each of the phases, represented in the histogram as separated peaks of sizes proportional to the G.sub.0 and G.sub.2 populations, and separation S phase population, aids in the prognosis of a patient's cancer development. More serious malignancy is indicated by increased S and G.sub.2 phase populations. Errors, e.g.

Abstract: A computerized specimen encoder for use with microscope analysis and pathological studies. The slide encoder is attached to the movable microscope stage, whereby X-Y plane movement and location, is correlated to examination of a specimen on an identified slide, with information marking and location being directly correspondingly written on computer storage media, during the examination. The information marking is in the form of computer generated indicia which are placed at a computer image location of the slide at predetermined time intervals. Subsequent use of the computer-stored information, coupled with the slide encoder, in a slide re-examination, permits independent retrieval of such information and location on the slide. The encoder device is provided with a grayscale marker which marks in varying shades of gray, ranging from white to black, the time spent by a slide screener on a particular portion of the specimen and the number of times spent viewing a particular portion of the specimen.

Abstract: A method for the accurate counting of DNA probe spots in cell nuclei wherein anomalies caused by a two dimensional measurement of a three dimensional cell sample are eliminated from evaluation. DNA probe spots in cell nuclei which are counted by means of Fluorescent In Situ Hybridization (FISH) include cells wherein probe spots of different contoured cells are overlaid or are detected as being adjacent one another with resultant erroneous diagnostic results such as with cancer detection or prognosis. A gating fluorescent value is determined by clusters of fluorescence in regions of non-anomalous values of fluorescence determined by plotting peak fluorescent value against area. The loci of the non-anomalous peak values cluster in specifically definable regions whereby fluorescent values for cells which deviate from the gating fluorescent value, are discounted in the preparation of histograms or other diagnostic measurements.

Abstract: A method of characterizing the chromosomes in a sample of cells by fixing the cell sample on a substrate, contacting the cell sample with a nucleic acid probe having a detectable label under conditions that allow the probe to hybridize preferentially to a chromosome in the cells to form a hybridized complex, optically detecting each labeled complex in the sample, defining a predetermined number of neighboring labeled complexes as a group, generating a distance parameter based on the distance between the position of a group and the position of the next neighboring labeled complex, and comparing the distance parameter for each group to a standard distance value to characterize the chromosomes in the cells of the sample.

Abstract: The invention relates to an apparatus and methods for generating multiparameter optical data that characterize a population of cells. The invention includes the steps of scanning the cell population with a beam to produce sets of digital data samples, each sample set of digital data representing multiparameter optical interactions from a specific location within the cell population; storing the digital data, e.g., in a computer memory; locating a cell within the population, e.g., by comparing the digital data to a preselected threshold value; defining a neighborhood around the digital data representing the located cell; estimating a background level for the neighborhood based upon digital data corresponding to locations outside the neighborhood; and correcting each of the samples corresponding to the neighborhood with the estimated neighborhood background level to generate the optical data.