A system for creating a contiguous digital image of a fluorescence microscope sample. In an embodiment, the system comprises a both a macro camera and a time delay integration (TDI) line scan camera. The system may also comprise a motorized stage, an illumination module, a light source, an excitatio
A system for creating a contiguous digital image of a fluorescence microscope sample. In an embodiment, the system comprises a both a macro camera and a time delay integration (TDI) line scan camera. The system may also comprise a motorized stage, an illumination module, a light source, an excitation filter, an objective lens, an emission filter, and at least one processor configured to assemble a plurality of digital images of portions of the fluorescence microscope sample, generated by the TDI line scan camera, into a contiguous digital image of at least a portion of the fluorescence microscope sample.
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1. A system for creating a contiguous digital image of a portion of a fluorescence microscope sample, the system comprising: a motorized stage configured to support a fluorescence microscope sample and move the fluorescence microscope sample at a substantially constant velocity;an illumination sourc
1. A system for creating a contiguous digital image of a portion of a fluorescence microscope sample, the system comprising: a motorized stage configured to support a fluorescence microscope sample and move the fluorescence microscope sample at a substantially constant velocity;an illumination source configured to apply oblique illumination to the fluorescence microscope sample on the motorized stage, wherein the illumination source comprises a light source configured to provide excitation light to a portion of the fluorescence microscope sample via an illumination path while the fluorescence microscope sample on the motorized stage is moving at substantially constant velocity;a macro camera configured to capture an image of the fluorescence microscope sample on the motorized stage during oblique illumination;an excitation filter in the illumination path;a time delay integration (TDI) line scan camera comprising a plurality of linear sensor arrays configured to generate a digital image stripe of a portion of the fluorescence microscope sample on the motorized stage while the sample is moving at substantially constant velocity;an objective lens positioned in an optical path between the fluorescence microscope sample on the motorized stage and the TDI line scan camera;an emission filter in the optical path; andat least one processor configured to assemble a plurality of digital image stripes, corresponding to a plurality of stripe regions of the fluorescence microscope sample, generated by the TDI line scan camera, into a contiguous digital image of at least a portion of the fluorescence microscope sample,wherein the plurality of digital image stripes are generated by (a) by the motorized stage, accelerating the fluorescence microscope sample from a substantially complete stop to the substantially constant velocity,(b) by the TDI line scan camera, generating a digital image stripe by sensing emission light, received at the plurality of linear sensor arrays via the optical path, from a stripe region of the fluorescence microscope sample,(c) by the motorized stage, decelerating the fluorescence microscope sample from the substantially constant velocity to the substantially complete stop, and(d) repeating steps (a) through (c) a plurality of times until the at least a portion of the fluorescence microscope sample has been digitized as the plurality of digital image stripes. 2. The system of claim 1, wherein the at least one processor is further configured to analyze image data generated by the macro camera to determine a scan area on the fluorescence microscope sample for the TDI line scan camera, prior to generating the plurality of digital images of portions of the fluorescence microscope sample using the TDI line scan camera. 3. The system of claim 2, wherein the image data comprises a plurality of pixels, and wherein analyzing the image data generated by the macro camera comprises, for each of the plurality of pixels, classifying the pixel as either tissue or not tissue based on an intensity of the pixel. 4. The system of claim 1, wherein the objective lens is also positioned in the illumination path, and wherein the system further comprises a dichroic mirror positioned in the illumination path between the objective lens and the light source and in the optical path between the objective lens and the TDI line scan camera. 5. The system of claim 4, wherein the dichroic mirror has wavelength-dependent reflectivity and transmission such that the excitation light from the light source reflects off a surface of the dichroic mirror toward the objective lens, and emitted light from the illuminated portion of the fluorescence microscope sample passes through the dichroic mirror toward the TDI line scan camera. 6. The system of claim 1, further comprising beam-shaping optics positioned in the illumination path, wherein the beam-shaping optics reshape an illumination area of the excitation light. 7. The system of claim 6, wherein the beam-shaping optics reshape an illumination area of the excitation light from a circular shape into an oval shape. 8. The system of claim 7, wherein the oval shape is a thin oval shape that approximates a rectangular area. 9. The system of claim 1, wherein the at least one processor is further configured to: (a) determine a current exposure time;(b) scan an image of a portion of the fluorescence microscope sample in accordance with the current exposure time;(c) calculate a logarithmic histogram of the scanned image;(d) determine a linear fit to said logarithmic histogram;(e) determine the intersection of the linear fit with the intensity axis of the logarithmic histogram;(f) compare the intersection to a predetermined range;(g) identify the current exposure time as the optimal exposure time if the intersection is within said predetermined range; and(h) adjust the current exposure time and repeat steps (b) through (g) if the intersection is not within said predetermined range. 10. The system of claim 1, wherein the excitation filter comprises a motorized wheel comprising a plurality of excitation filters, wherein each of the plurality of excitation filters narrows broadband excitation light from the light source into a single band of excitation light. 11. The system of claim 10, wherein the emission filter comprises a motorized wheel comprising a plurality of emission filters. 12. The system of claim 11, wherein the at least one processor is further configured to: analyze image data generated by the macro camera to identify a plurality of fluorochromes on the fluorescence microscope sample; andfor each of the plurality of fluorochromes, identify a combination of the plurality of excitation filters and the plurality of emission filters with which to scan the fluorescence microscope sample using the motorized stage and TDI line scan camera. 13. The system of claim 1, wherein one or both of the excitation filter and the emission filter comprises a plurality of filters, and wherein the at least one processor is further configured to control the plurality of filters to, in conjunction with the motorized stage and the TDI line scan camera, digitize the at least a portion of the fluorescence microscope sample for each of a plurality of wavelengths to produce a contiguous digital image for each of the plurality of wavelengths. 14. The system of claim 13, wherein the at least one processor is further configured to store the contiguous digital images for the plurality of wavelengths as a single image file comprising a base layer and one or more subsequent layers, wherein the base layer comprises the contiguous digital image for each of the plurality of wavelengths at an original-scan resolution, and wherein each of the one or more subsequent layers comprises the contiguous digital image for each of the plurality of wavelengths at a sub-sampled resolution. 15. The system of claim 1, wherein the excitation filter comprises a plurality of single-band excitation filters, wherein each of the plurality of single-band excitation filters narrows broadband excitation light from the light source into a single band of excitation light, and wherein the emission filter comprises a multiple-band emission filter that narrows light received by the emission filter into multiple bands of emission light. 16. The system of claim 15, wherein repeating steps (a) through (c) comprises, for each of the plurality of stripe regions of the fluorescence microscope sample: repeating steps (a) through (c) a plurality of times; and,between each iteration of steps (a) through (c) for the stripe region, moving a different one of the plurality of single-band excitation filters into the illumination path. 17. The system of claim 1, wherein the motorized stage moves the fluorescence microscope sample at the substantially constant velocity in a direction that is perpendicular to each of the plurality of linear sensory arrays, such that each of the plurality of stripe regions of the fluorescence microscope sample is sensed by each of the plurality of linear sensory arrays to generate multiple exposures of each of the plurality of stripe regions. 18. The system of claim 17, wherein, for each of the plurality of stripe regions, the multiple exposures for the stripe region are combined to create a single image stripe corresponding to the stripe region. 19. The system of claim 18, wherein the at least one processor aligns adjacent ones of the plurality of image stripes by: calculating a contrast distribution for an overlap area of the adjacent image stripes;identifying a contrast peak in the contrast distribution; and aligning the adjacent image stripes based on pixels corresponding to a band around the contrast peak.
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