Francis S Cheng

US Patent:

8538733, Sep 17, 2013

Filed:

Jan 23, 2009

Appl. No.:

12/359241

Inventors:

Francis T. Cheng - Palo Alto CA, US
Casey R. McFarland - San Francisco CA, US

Assignee:

Life Technologies Corporation - Carlsbad CA

International Classification:

H04B 15/00

US Classification:

702195, 374 1, 374 43, 374137, 436147, 702 19, 702 85, 702130

Abstract:

Methods are provided that operate on raw dissociation data and dissociation curves to generate calibrations of the detected data and to further improve analysis of the data. The data can be taken from each support region of a multi-region platform, for example, from each well of a multi-well plate. Each support region can be loaded with portions of the same sample. In some embodiments, a dissociation curve correction can be calibrated for the sample, prior to a run of an experiment using such sample. In some embodiments, a method is provided for generating a melting transition region of dissociation curves that show the melting characteristics of the sample. In some embodiments, dye temperature dependence correction can be performed on the dissociation curve data to further improve analysis. In some embodiments, a feature vector can be derived from the melt data, and the feature vector can be used to further improve genotyping analysis of the dissociation curves.

US Patent:

20090037117, Feb 5, 2009

Filed:

Jan 25, 2008

Appl. No.:

12/020369

Inventors:

Francis T. Cheng - Palo Alto CA, US

Assignee:

Applera Corporation - Foster City CA

International Classification:

G06F 19/00
G06F 15/00

US Classification:

702 20, 702189

Abstract:

Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.

US Patent:

20110105345, May 5, 2011

Filed:

Aug 2, 2010

Appl. No.:

12/848967

Inventors:

Francis T. Cheng - Palo Alto CA, US
Chengyong Yang - Foster City CA, US
Casey R. McFarland - San Francisco CA, US
Ying Wang - Chicago IL, US

Assignee:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA

International Classification:

C40B 30/02

US Classification:

506 8

Abstract:

The present application provides for various embodiments of methods for the analysis of high resolution melt (HRM) curve data; where statistical assay variations in melt curve data may result from system noise in an analysis system. Such system noise may arise from various sources, such as the thermal non-uniformity of a thermocycler block in a thermal cycler apparatus, a detection system, etc. Additionally, various methods for the analysis of HRM curve data may provide an identification of a sample without the need for a user inputted information.

US Patent:

60941529, Jul 25, 2000

Filed:

Dec 23, 1998

Appl. No.:

9/220872

Inventors:

Francis T. Cheng - Palo Alto CA

Assignee:

Siemens Medical Systems, Inc. - Iselin NJ

International Classification:

H03M 100

US Classification:

341132

Abstract:

A robust histogram analysis algorithm is used in accordance with the present invention to control the electronic portal image analog to digital (A/D) window such that the acquired images will have sufficient contrast for their uses in radiotherapy. The algorithm includes setting an initial estimate of a region of interest within a histogram, the histogram including pixel counts and pixel values related to the pixel counts, and determining two dominant peaks inside the region of interest. One of the two dominant peaks is below a predetermined value and the other of the two dominant peaks is between the predetermined value and a second predetermined value. If the one dominant peak is more than two times the standard deviation of the other dominant peak, then a first local minimum to the right of the one dominant peak will be the revised boundary. If the other dominant peak is more than two times the standard deviation of the one dominant peak, then a first local minimum to the left of the other dominant peak will be the revised boundary. Otherwise the average value of the two dominant peaks will be the revised boundary.

US Patent:

61480606, Nov 14, 2000

Filed:

Oct 13, 1998

Appl. No.:

9/172709

Inventors:

William F. Collins - Clayton CA
Francis Cheng - Palo Alto CA

Assignee:

Siemens Medical Systems, Inc. - Iselin NJ

International Classification:

A61N 510

US Classification:

378 65

Abstract:

Method and system aspects for integrated automatic exposure control for portal imaging in radiotherapy are described. In an exemplary method aspect, the method includes controlling scanning and blanking of a target of a camera pick-up tube to capture an initial image, and analyzing the initial image to establish an initial image intensity. The method further includes utilizing the initial image intensity to determine a time for scanning a next image, and combining a scan of the next image with the initial image to produce a portal image with a maximized signal to noise ratio.

US Patent:

20190300936, Oct 3, 2019

Filed:

Apr 12, 2019

Appl. No.:

16/382294

Inventors:

- Carlsbad CA, US
Geoffrey DAHLHOFF - Menlo Parl CA, US
Kevin MAHER - Woodside CA, US
Ming Song CHEN - Singapore, SG
Gary LIM - San Francisco CA, US
Ronald DANEHY - Shirley MA, US
David FORTESCUE - San Francisco CA, US
Ming SHEN - Singapore, SG
Woon Liang Soh - Singapore, SG
Francis T. CHENG - Palo Alto CA, US
Ruoyun WU - Singapore, SG
Thiam Chye LEE - Singapore, SG
Gary A. CHAPPELL - San Francisco CA, US
Chee Kiong LIM - Singapore, SG
Jeff DERE - Saratoga CA, US
Ted E. STRAUB - Burlingame CA, US
Jorge FONSECA - East Palo Alto CA, US
Kuan Moon BOO - Singapore, SG
Soo Yong LAU - Singapore, SG

Assignee:

LIFE TECHNOLOGIES CORPORATION - Carlsbad CA

International Classification:

C12Q 1/686
B01L 3/00
B01L 7/00

Abstract:

A biological analysis system is provided. The system comprises an interchangeable assembly configured to accommodate any one of a plurality of sample holders, each respective sample holder configured to receive a plurality of samples. The system also includes a control system configured to cycle the plurality of samples through a series of temperatures. The system further includes an optical system configured to detect fluorescent signals emitted from the plurality of samples. The optical system, in particular, can comprise a single field lens, an excitation source, an optical sensor, and a plurality of filter components. The excitation source can be one or more light emitting diodes. The field lends can be a bi-convex lens.

US Patent:

20180314788, Nov 1, 2018

Filed:

Apr 27, 2018

Appl. No.:

15/965380

Inventors:

- Carlsbad CA, US
Francis T. Cheng - Palo Alto CA, US

Assignee:

Applied Biosystems, LLC - Carlsbad CA

International Classification:

G06F 19/10
C12Q 1/6844

Abstract:

Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.

US Patent:

20170161429, Jun 8, 2017

Filed:

Nov 14, 2016

Appl. No.:

15/350444

Inventors:

- Carlsbad CA, US
Jeffrey Marks - Mountain View CA, US
Francis Cheng - Palo Alto CA, US
Thomas Wessel - Pleasanton CA, US

International Classification:

G06K 9/00

Abstract:

A method for calibrating a biological instrument is provided. The method comprises the steps of acquiring an image of at least one biological sample array, determining a first region of interest within the image, wherein the first region of interest comprises a first plurality of locations on the at least one biological array; and identifying within the first region of interest, a plurality of image elements associated with each of the first plurality of locations on the at least one biological array.