Image analysis – Applications
Reexamination Certificate
2000-06-01
2003-03-04
Johns, Andrew W. (Department: 2721)
Image analysis
Applications
Reexamination Certificate
active
06529612
ABSTRACT:
BACKGROUND OF THE INVENTION
I. Field of the Invention
The present invention relates to a computer controlled system which acquires, stores and analyzes crystal images and other parameters relevant to the crystals, or microscopic details of other specimens.
II. Description of the Prior Art
In many chemical, pharmaceutical and medical applications crystals, e.g. protein crystals, are grown in trays for subsequent evaluation by a lab technician or scientist (hereinafter collectively referred to as “technician”). In evaluating the crystals once grown, the lab technician examines the crystals under the microscope and then visually evaluates or rates individual crystals. The straightness of the crystal edges, size of the crystal, presence or absence of flaws in the crystal as well as other crystal parameters are used by the technician in his or her rating process. The technician may also maintain notes of other parameters, such as pH, crystal growing time, temperature, et cetera, which are relevant to the particular crystal.
In some instances, the technician will take and maintain a photograph of the particular crystal under examination. The photograph is then stored along with the notes relevant to the particular crystals in the particular tray.
This previously known system for evaluating and rating crystals is disadvantageous for a number of reasons. Most prominently, the crystal evaluation and rating system is labor intensive and, thus, not only slow and expensive in labor costs, but also tedious for the technician.
A still further disadvantage of these previously known systems is that the photographic record used for the examined crystal is expensive in material costs from the photographic process. Furthermore, photographs by their very nature are easily damaged and also deteriorate over time.
A still further disadvantage of the previously known method for evaluating and rating crystals is that no efficient means or system has been previously known for cross-referencing the various crystals and crystal parameters relative to each other. Instead, the photographic picture as well as the other parameters relevant to the particular picture are simply maintained separately from the crystal specimens.
SUMMARY OF THE PRESENT INVENTION
The present invention provides a system utilizing a digital computer which overcomes all of the above-mentioned disadvantages of acquiring, storing and evaluating crystals, such as protein crystals, or microscopic details of other specimens.
In brief, the present invention utilizes a video camera which provides a digital output signal representative of an object, in this case crystals maintained within a tray, positioned within its focal window. Preferably, a central computer controls a movable stage to sequentially position trays in the focal window. The camera is operated under the control of a central computer which not only activates the initiation of the image acquisition by the camera, but also stores the output from the camera in digital form on data storage media. Preferably, the optical image from the video camera is stored on removable data storage media, such as a JAZZ™ drive, ZIP™ drive or CD ROM, etc.
In addition to storing the acquired optical image from the video camera, the technician, via a computer keyboard, mouse or other computer input means, also inputs data corresponding to parameters relevant to the particular crystal specimen under examination. Such parameters can include, for example, the pH, temperature, duration of crystal growth, et cetera for the particular crystal specimen. Additionally, the computer software preferably provides input template configurations to simplify the data input of the parameters by the technician and thus avoid or at least minimize the redundant input of information for different trays having similar parameters.
The various stored parameters may also be stored with the optical image on the data storage media. However, more preferably, the parameters relevant to the crystal specimens are stored in a database on one data storage media, for example a hard drive, with an index or record pointer to the appropriate image stored on the removable drive with the optical images. In this fashion, a large database of the various crystal parameters may be maintained and analyzed relative to each other with access to the optical images always available as required or desired.
Following acquisition of the optical image as well as the other crystal parameters, the computer is programmed to analyze the optical image for the presence and count of protein crystals. As a part of the evaluation, the computer program identifies the edges of the crystal, filling in any gaps of the edge where necessary, and than analyzes the resulting data for its perimeter symmetry and roughness, straightness, crystal size, presence or absence of defects and center of gravity. The crystal rating is then stored in the data base.
Preferably, the present invention utilizes a fast T-squared filer during its analysis of the optical image in order to grade the crystal. Alternatively, the present invention utilizes a 3×3 edge detection filter during its analysis of the optical image in order to identify the crystal edges, then the image is converted to a binary image with a threshold of approximately 40 on a scale of 0 to 255 to reduce image artifacts. The size of the crystal is determined via perimeter connectivity analysis. Objects with a small perimeter are excluded. The net resulting image is analyzed for its roughness which is a measure of the perimeter divided by the convex perimeter. This metric is used to isolate the crystal from the drop boundary and other artifacts. The center of gravity is calculated on the remaining data to pinpoint the crystals.
Alternatively, other methods may also be used to grade the crystal based upon metrics such as edge straightness, aspect ratio, surface clarity, polygon formation, color etc. These methods include the use of traditional spatial filters such as highpass, lowpass, Butterworth, homomorphic, Sobel, Laplacian, etc. Probabilistic restoration such as least mean square (Wiener) filters, fast T-squared filters, spatial transformations, frequency transformations, etc. can be used. Edge linking and boundary detection using Hough Transforms, “Line-filler” filters, thresholding, etc. can be used. Representation and description using Fourier descriptors, topological descriptors, texture descriptors, statistical descriptors, moments, mathematical morphological descriptors, etc. can be used. Recognition using minimum distance classifiers, correlation classifiers, statistical classifiers, Bayesian classifiers, neural networks, genetic algorithms, etc. can be used.
REFERENCES:
patent: 4900147 (1990-02-01), Bowley et al.
patent: 5076698 (1991-12-01), Smith et al.
patent: 5124935 (1992-06-01), Wallner et al.
patent: 5193685 (1993-03-01), Trevithick
patent: 5544254 (1996-08-01), Hartley et al.
Christopher Gayle K.
Delucas Lawrence J.
Gester Thomas E.
Hamrick David T.
Rosenblum William M.
Diversified Scientific, Inc.
Gifford, Krass, Groh Sprinkle, Anderson & Citkowski, P.C.
Johns Andrew W.
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