Abstract: Methods of treating a subject with cancer with CD8 T cell-mediated immune therapy are provided. The methods include measuring an amount of CXCR3-positive T cells in a peripheral blood sample or a tumor sample from a subject with cancer following treatment of the subject with at least one dose of the CD8 T cell-mediated therapy and comparing the amount of CXCR3-positive T cells in the sample to a control. Responsiveness of the cancer to the CD8 T cell-mediated therapy is predicted based on whether there is an increase or decrease in the amount of CXCR3-positive T cells in the sample. Methods further including treating the subject with at least one additional dose of the CD8 T cell-mediated immune therapy are also provided.

Abstract: An apparatus for generating structured illumination images, comprising a housing; imaging optics mounted within the housing, the imaging optics configured to focus illumination from an illumination source such that an in-focus pattern of light corresponding to a pattern on a photomask is projected onto a sample; a reflector mounted within the housing and configured to reflect the illumination to a sample; a filter apparatus, comprising one or more filters mounted within the housing, the filter apparatus configured to allow only emissions from the illuminated sample to pass through to the sensor; and mounting features on the housing, the mounting features configured to allow the apparatus to be installed within an imaging system.

Abstract: An apparatus for generating composite confocal images, comprising: an imaging apparatus configured to generate illumination; a sample stage configured to hold a sample to be illuminated by the illumination, wherein the illumination causes the sample to generate emissions that can be detected and used to image the sample, the sample stage configured to move the sample to a plurality of positions during the imaging process; and a vibration mechanism coupled with the sample stage, the motor configured to vibrate the stage after the stage moves the sample for a vibration period.

Abstract: A method for calibrating an imaging system can include at least the following method acts: illuminating a sample through a pinhole mask using an excitation light; capturing an image of the sample using a sensor; converting the image into data; in a processing module: filtering the data using a known spacing of pinholes in the pinhole mask to obtain filtered data that corresponds to the known spacing, using a threshold to identify regions of the filtered data that are bright enough to be associated with a pinhole, calculating the centroids of the regions, and fitting a known pattern for the pinhole mask to the regions in order to identify the best fit data for the filtered data; and storing, in a storage medium, the best fit data for use in a subsequent confocal capture routine.

Abstract: A method for generating a composite image obtained in a fluorescence imaging system, comprising: determining the physical locations of a pinhole mask relative to a sample required to construct a full composite confocal image; generating in a control module a randomized order for the determined physical locations; moving the photomask or the sample to the determined physical locations in the randomized order under control of the control module and using a translation stage; illuminating the sample through the photomask using an excitation light; capturing a plurality of images at each of the physical locations using a sensor in order to generate a set of data points; using the randomized order to generate a composite image based on the set of data points and measuring the brightness of at least some of the data points; and adjusting the brightness of some of the set of data points.

Abstract: A method for calibrating an imaging system, comprising: illuminating a sample through a pinhole mask using an excitation light; capturing an image of the sample using a sensor; converting the image into data; in a processing module: filtering the data using known spacing of pinholes in the pinhole mask to obtain data that corresponds to the spacing, using a threshold to identify regions of the remaining data that are bright enough to be associated with a pinhole, calculating the centroids of the regions, and fitting a known pattern for the pinhole mask to the regions in order to identify the best fit for the data; and storing, in a storage medium, the best fit data for use in a subsequent confocal capture routine.

Abstract: An apparatus for generating composite confocal images, comprising: an imaging apparatus configured to generate illumination; a sample stage configured to hold a sample to be illuminated by the illumination, wherein the illumination causes the sample to generate emissions that can be detected and used to image the sample, the sample stage configured to move the sample to a plurality of positions during the imaging process; and a vibration mechanism coupled with the sample stage, the motor configured to vibrate the stage after the stage moves the sample for a vibration period.

Abstract: A method for generating a composite image obtained in a fluorescence imaging system, comprising: determining the physical locations of a pinhole mask relative to a sample required to construct a full composite confocal image; generating in a control module a randomized order for the determined physical locations; moving the photomask or the sample to the determined physical locations in the randomized order under control of the control module and using a translation stage; illuminating the sample through the photomask using an excitation light; capturing a plurality of images at each of the physical locations using a sensor in order to generate a set of data points; using the randomized order to generate a composite image based on the set of data points and measuring the brightness of at least some of the data points; and adjusting the brightness of some of the set of data points.

Abstract: An apparatus for generating structured illumination images, comprising a housing; imaging optics mounted within the housing, the imaging optics configured to focus illumination from an illumination source such that an in-focus pattern of light corresponding to a pattern on a photomask is projected onto a sample; a reflector mounted within the housing and configured to reflect the illumination to a sample; a filter apparatus, comprising one or more filters mounted within the housing, the filter apparatus configured to allow only emissions from the illuminated sample to pass through to the sensor; and mounting features on the housing, the mounting features configured to allow the apparatus to be installed within an imaging system.