Affymetrix, Inc.

Eric E McKenzie

Mark R Jones

Nathan K Weiner

David Bradbury

Christopher Miles

Patrick Odoy

David A Stura

Albert Bukys

Herman Deweerd

Thomas P Regan

James T Overbeck

Tim J Woolaver

Roger DiPaolo

Joel M Katz

Eric Schultz

Ksenia Oleink-Ovod

Peter D Honkanen

Shantanu V Kaushikkar

Timothy J Woolaver

Oleinik-Ovod Ksenia

Ksenia Oleinik-Ovod

Erik Schultz

John C Stephens

An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

System and method for scanning of probe arrays

System, method, and product for scanning of biological materials

A system is described for automatic retrieval of microplates from a carousel. The system includes an effector arm that retrieves a selected microplate from the carousel, a microplate retainer that receives the selected microplate from the effector arm, and a controller that directs the effector arm to the carousel for retrieval of the selected microplate and directs the effector arm to the microplate retainer so that it may receive the selected microplate. The carousel may revolve around a vertical axis. A system also is described for washing depositing elements used to spot biological materials on a substrate. Graphical user interfaces also are described for enabling a user to determine which microplates will be used to provide biological probe materials, and in what patterns those probe materials should be deposited on the substrate. The interfaces enable the user to place multiple fractions of biological materials on a same location on a substrate. Also described are graphical user interfaces that present a user with the options to select a first microplate having a plurality of wells, associate at least one probe material with one or more of the wells, and associate one or more locations on one or more substrates with the one or more wells.

High throughput microarray spotting system and method

Systems, methods, and computer program products are described for adjusting the gain of a scanner. The scanner includes one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain. One described method includes receiving a user-selected gain value, adjusting the first gain based on a first portion of the user-selected gain value, and adjusting the second gain based on a second portion of the user-selected gain value. Another described method includes selecting an auto-gain value, adjusting the first gain based on a first portion of the auto-gain value, adjusting the second gain based on a second portion of the auto-gain value, causing the scanner to collect sample pixel intensity values, determining a comparison measure based on comparing the sample pixel intensity values to desired pixel intensity values, and adjusting the auto-gain value based on the comparison measure.

System, method, and computer software product for gain adjustment in biological microarray scanner

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Malden, MA, United States of America

Eric E McKenzie