Digital microscope slide scanning system and methods
Provided herein are systems methods including a design of a microscope slide scanner for digital pathology applications which provides high quality images and automated batch-mode operation at low cost. The instrument architecture is advantageously based on a convergence of high performance, yet low cost, computing technologies, interfaces and software standards to enable high quality digital microscopy at very low cost. Also provided is a method based in part on a stitching method that allows for dividing an image into a number of overlapping tiles and reconstituting the image with a magnification without substantial loss of accuracy. A scanner is employed in capturing snapshot images. The method allows for overlapping images captured in consecutive snapshots.
1. A slide rack auto-loader for use in a digital microscope slide scanning system comprising:
a first user removable rack comprising multiple slide holders;
a first laser that directs a first amount of light toward the first user removable rack; and
a first detector that detects a second amount of light after the light from the first laser has been directed toward the first user removable rack, and wherein a determination is made that at least one slide is present in the slide holder or that no slide is present in the slide holder, based on the second amount of light sensed by the detector.
2. The slide rack auto-loader of claim 1 ,
wherein the holders are arranged in a basket that holds 20 slides per basket and are arranged with two stacked baskets in four columns.
3. The slide rack auto-loader of claim 1 , wherein
the second amount of light is light scattered from the at least one slide in the slide holder and the first detector detects the second amount of light, and wherein a determination is made as to whether one slide or two slides are present in the slide holder based on the light scattered from the at least one slide.
4. The slide rack auto-loader of claim 2 , further comprising:
4 laser/detector pairs to scan down each of the 4 columns of slides.
5. The slide rack autoloader of claim 1 wherein as the first user removable rack is translated vertically, each slide is sensed and the position recorded.
6. The slide rack auto-loader of claim 5 , wherein the positions are used for:
determining the required vertical height to safely extract the slide from the rack for scanning.
7. A slide rack autoloader comprising:
a sensor system to accurately determine a slide's position for safe slide extraction from rack to scanning system; and
at least one slide rack for holding the slide.
8. The slide rack autoloader of claim 5 , wherein at least one of an x, y, and z position is recorded.
9. The slide rack autoloader of claim 1 , further comprising:
A/D converter on a microprocessor, wherein the first detector produces an analog voltage change, corresponding to the second amount of light detected by the first detector, wherein the second amount of light is fed to the A/D converter, wherein the A/D converts the signal to a digital signal that is processed by the microprocessor, and wherein the microprocessor determines at least one of a width and a height of the digital signal.
10. The slide rack autoloader of claim 1 , wherein the second amount of light corresponds to a light signal having a shape, and wherein the shape of the light signal is used to determine at least one of whether (a) the at least one slide is in the slot holder; (b) whether two slides are loaded in the same slot holder; and (c) whether the at least one slide is tilted within the slot holder.
11. The slide rack loader of claim 1 , wherein the second amount of light corresponds to a light pulse, and wherein when the width of the pulse determines that the at least one slide is not present.
12. The slide rack loader of claim 1 , wherein the second amount of light corresponds to a light pulse, and wherein when the width of the pulse determines an erroneously loaded slide.
13. A method for recognizing slides in a slide rack for use in a digital microscope slide scanning system, comprising:
directing a first amount of light toward the slide rack;
detecting a second amount of light present after the light from the first laser has been directed toward the slide rack; and
determining that at least one slide is present in the slide holder or that no slide is present in the slide holder, based on the second amount of light sensed by the detector.
14. The slide rack auto-loader of claim 1 , wherein
the second amount of light is light scattered from the at least one slide in the slide holder and the first detector detects the second amount of light, and wherein a determination is made as to whether one or more slides are present in the slide holder based on the light scattered from the at least one slide.