Auto-focus methods and systems for digital imaging using multi-spectral trajectories
A method and associated method and computer program product for acquiring focused images of a specimen on a slide, by determining optimal scanning trajectories. The method includes capturing a relatively low magnification image of the slide to locate the specimen, forming a grid that includes an arrangement of grid points, overlaying at least part of the grid over a field of view that covers at least part of the specimen, capturing a relatively high magnification Z-stack of images of the specimen within the field of view, determining a best focus for each grid point within said at least part of the grid to form a resulting grid of three dimensional points, and based on the resulting grid, determining one or more three dimensional scanning trajectories.
1. A method comprising:
accessing a first image depicting at least part of a specimen;
selecting a first color from a set of colors depicted in the first image;
identifying a first plurality of grid points in the first image, wherein each grid point of the first plurality of grid points correspond to the first color;
determining, for each grid point of the first plurality of grid points, a z-axis value corresponding to the grid point, wherein the z-axis value identifies a vertical position of a lens assembly of a scanning system for capturing, at a particular focus, a portion of the first image represented by the grid point;
generating a first scanning trajectory that connects the z-axis values of the first plurality of grid points; and
outputting the first scanning trajectory, wherein processing of the first scanning trajectory triggers the scanning system to generate a second image based on the lens assembly traversing through the vertical positions indicated by the z-axis values of the first scanning trajectory.
2. The method of claim 1 , further comprising:
selecting a second color from the set of colors depicted in the first image;
identifying a second plurality of grid points in the first image, wherein each grid point of the second plurality of grid points correspond to the second color;
determining, for each grid point of the second plurality of grid points, a z-axis value corresponding to the grid point;
generating a second scanning trajectory that connects the z-axis values of the second plurality of grid points; and
outputting the second scanning trajectory.
3. The method of claim 2 , further comprising extending the first scanning trajectory into the second scanning trajectory to generate a third scanning trajectory, wherein processing of the third scanning trajectory triggers the scanning system to generate a third image based on the lens assembly traversing through the vertical positions indicated by the z-axis values of the first scanning trajectory and the second scanning trajectory.
4. The method of claim 2 , wherein the first color indicates a presence of a first biomarker depicted in the first image and the second color indicates a presence of a second biomarker depicted in the second image.
5. The method of claim 1 , wherein the second image includes one or more image portions that depict the first color at the particular focus.
6. The method of claim 1 , wherein determining the z-axis value corresponding to the grid point includes:
generating a plurality of Z-stack images for the grid point;
determining, for each Z-stack image of the plurality of Z-stack images, an image gradient value corresponding to the first color;
selecting a Z-stack image of the plurality of Z-stack images that is associated with a highest image gradient value corresponding to the first color; and
determining the z-axis value based on a position of the lens assembly at which the selected Z-stack image was generated.
7. The method of claim 1 , further comprising:
overlaying a grid over the first image; and
identifying the first plurality of grid points relative to the grid overlaid over the first image.
8. A system comprising:
one or more processors; and
a memory having stored thereon instructions that, upon execution by the one or more processors, cause the one or more processors to:
access a first image depicting at least part of a specimen;
select a first color from a set of colors depicted in the first image;
identify a first plurality of grid points in the first image, wherein each grid point of the first plurality of grid points correspond to the first color;
determine, for each grid point of the first plurality of grid points, a z-axis value corresponding to the grid point, wherein the z-axis value identifies a vertical position of a lens assembly of a scanning system for capturing, at a particular focus, a portion of the first image represented by the grid point;
generate a first scanning trajectory that connects the z-axis values of the first plurality of grid points; and
output the first scanning trajectory, wherein processing of the first scanning trajectory triggers the scanning system to generate a second image based on the lens assembly traversing through the vertical positions indicated by the z-axis values of the first scanning trajectory.
9. The system of claim 8 , wherein the instructions further cause the one or more processors to:
select a second color from the set of colors depicted in the first image;
identify a second plurality of grid points in the first image, wherein each grid point of the second plurality of grid points correspond to the second color;
determine, for each grid point of the second plurality of grid points, a z-axis value corresponding to the grid point;
generate a second scanning trajectory that connects the z-axis values of the second plurality of grid points; and
output the second scanning trajectory.
10. The system of claim 9 , wherein the instructions further cause the one or more processors to extend the first scanning trajectory into the second scanning trajectory to generate a third scanning trajectory, wherein processing of the third scanning trajectory triggers the scanning system to generate a third image based on the lens assembly traversing through the vertical positions indicated by the z-axis values of the first scanning trajectory and the second scanning trajectory.
11. The system of claim 9 , wherein the first color indicates a presence of a first biomarker depicted in the first image and the second color indicates a presence of a second biomarker depicted in the second image.
12. The system of claim 8 , wherein the second image includes one or more image portions that depict the first color at the particular focus.
13. The system of claim 8 , wherein determining the z-axis value corresponding to the grid point includes:
generating a plurality of Z-stack images for the grid point;
determining, for each Z-stack image of the plurality of Z-stack images, an image gradient value corresponding to the first color;
selecting a Z-stack image of the plurality of Z-stack images that is associated with a highest image gradient value corresponding to the first color; and
determining the z-axis value based on a position of the lens assembly at which the selected Z-stack image was generated.
14. The system of claim 8 , wherein the instructions further cause the one or more processors to:
overlay a grid over the first image; and
identify the first plurality of grid points relative to the grid overlaid over the first image.
15. A computer program product tangibly embodied in a non-transitory machine-readable storage medium, including instructions configured to cause one or more data processors to perform actions including:
accessing a first image depicting at least part of a specimen;
selecting a first color from a set of colors depicted in the first image;
identifying a first plurality of grid points in the first image, wherein each grid point of the first plurality of grid points correspond to the first color;
determining, for each grid point of the first plurality of grid points, a z-axis value corresponding to the grid point, wherein the z-axis value identifies a vertical position of a lens assembly of a scanning system for capturing, at a particular focus, a portion of the first image represented by the grid point;
generating a first scanning trajectory that connects the z-axis values of the first plurality of grid points; and
outputting the first scanning trajectory, wherein processing of the first scanning trajectory triggers the scanning system to generate a second image based on the lens assembly traversing through the vertical positions indicated by the z-axis values of the first scanning trajectory.
16. The computer program product of claim 15 , wherein the instructions further cause the one or more data processors to perform actions including:
selecting a second color from the set of colors depicted in the first image;
identifying a second plurality of grid points in the first image, wherein each grid point of the second plurality of grid points correspond to the second color;
determining, for each grid point of the second plurality of grid points, a z-axis value corresponding to the grid point;
generating a second scanning trajectory that connects the z-axis values of the second plurality of grid points; and
outputting the second scanning trajectory.
17. The computer program product of claim 16 , wherein the instructions further cause the one or more data processors to perform actions including extending the first scanning trajectory into the second scanning trajectory to generate a third scanning trajectory, wherein processing of the third scanning trajectory triggers the scanning system to generate a third image based on the lens assembly traversing through the vertical positions indicated by the z-axis values of the first scanning trajectory and the second scanning trajectory.
18. The computer program product of claim 16 , wherein the first color indicates a presence of a first biomarker depicted in the first image and the second color indicates a presence of a second biomarker depicted in the second image.
19. The computer program product of claim 15 , wherein the second image includes one or more image portions that depict the first color at the particular focus.
20. The computer program product of claim 15 , wherein determining the z-axis value corresponding to the grid point includes:
generating a plurality of Z-stack images for the grid point;
determining, for each Z-stack image of the plurality of Z-stack images, an image gradient value corresponding to the first color;
selecting a Z-stack image of the plurality of Z-stack images that is associated with a highest image gradient value corresponding to the first color; and
determining the z-axis value based on a position of the lens assembly at which the selected Z-stack image was generated.