WO2015089564A4 - Thickness estimation for microscopy - Google Patents
Thickness estimation for microscopy Download PDFInfo
- Publication number
- WO2015089564A4 WO2015089564A4 PCT/AU2014/001147 AU2014001147W WO2015089564A4 WO 2015089564 A4 WO2015089564 A4 WO 2015089564A4 AU 2014001147 W AU2014001147 W AU 2014001147W WO 2015089564 A4 WO2015089564 A4 WO 2015089564A4
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- specimen
- region
- interest
- patches
- thickness parameter
- Prior art date
Links
Classifications
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01B—MEASURING LENGTH, THICKNESS OR SIMILAR LINEAR DIMENSIONS; MEASURING ANGLES; MEASURING AREAS; MEASURING IRREGULARITIES OF SURFACES OR CONTOURS
- G01B9/00—Measuring instruments characterised by the use of optical techniques
- G01B9/04—Measuring microscopes
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01B—MEASURING LENGTH, THICKNESS OR SIMILAR LINEAR DIMENSIONS; MEASURING ANGLES; MEASURING AREAS; MEASURING IRREGULARITIES OF SURFACES OR CONTOURS
- G01B21/00—Measuring arrangements or details thereof, where the measuring technique is not covered by the other groups of this subclass, unspecified or not relevant
- G01B21/02—Measuring arrangements or details thereof, where the measuring technique is not covered by the other groups of this subclass, unspecified or not relevant for measuring length, width, or thickness
- G01B21/08—Measuring arrangements or details thereof, where the measuring technique is not covered by the other groups of this subclass, unspecified or not relevant for measuring length, width, or thickness for measuring thickness
-
- G—PHYSICS
- G02—OPTICS
- G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
- G02B21/00—Microscopes
- G02B21/36—Microscopes arranged for photographic purposes or projection purposes or digital imaging or video purposes including associated control and data processing arrangements
- G02B21/365—Control or image processing arrangements for digital or video microscopes
- G02B21/367—Control or image processing arrangements for digital or video microscopes providing an output produced by processing a plurality of individual source images, e.g. image tiling, montage, composite images, depth sectioning, image comparison
Abstract
A method, of detemining at least one thickness parameter of a specimen from a stack of images of the specimen obtained from a microscope at a series of depths is disclosed. The method selects (340), within a region of interest, sets (850) of patches at a plurality of corresponding transverse locations in each image within the stack of images. A depth value is determined (350) at each transverse location from a set of contrast metrics computed for the set of patches at the transverse location, and the method determines (380) at least one thickness parameter for the specimen at the region of interest from at least a distribution (700) of the determined depth values.
Claims
1. A method of determining at least one thickness parameter of a specimen from a stack of images of the specimen obtained from a microscope at a series of depths , said method comprising:
determining, within a region of interest, sets of patches at a plurality of corresponding transverse locations in each image within the stack of images;
selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the set of patches at the transverse location; and
determining at least one thickness parameter for the specimen at the region of interest from at least a distribution of the selected depth values across the plurality of transverse locations of the region of interest.
2. A method according to claim 1, further comprising forming the distribution from depth values determined at different transverse locations across the specimen.
3. A method according to claim 2, wherein the forming of the distribution comprises determining outlier depth values that exceed a predetermined corresponding thickness parameter and removing the outlier depth values from the distribution before the determining of the at least one revised thickness parameter.
4. A method according to claim 3, wherein the predetermined corresponding thickness parameter is determined at an image level larger than the patches.
5. A method of determining at least one thickness parameter of a specimen from a stack of images of the specimen captured at a series of depths, said method comprising:
determining, within a region of interest, a patch at a corresponding location in each image within the stack of images to form a set of patches;
determining at least one initial thickness parameter of the specimen at the selected region of interest based on a set of contrast metrics computed for the set of patches;
determining sets of sub-patches at a plurality of corresponding transverse locations
within each patch in the set of patches;
selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the sub-patches at the transverse location; and
determining at least one revised thickness parameter for the specimen at the region of interest from a distribution of the selected depth values across the plurality of transverse locations of the region of interest and the initial thickness parameter.
6. A method according to claim 5 wherein the thickness parameter is selected from the group consisting of a thickness of the specimen, a location of a top surface of the specimen, and a location of a bottom surface of the specimen.
7. A method according to claim 5, further comprising determining outlier depth values that exceed a corresponding thickness parameter and removing the outlier depth values from the distribution before the determining of the at least one revised thickness parameter.
8. A method according to claim 7, wherein the corresponding thickness parameter comprises the initial thickness parameter.
9. A method according to claim 7, wherein the corresponding thickness parameter comprises a value of an upper or lower percentile of determined depth values.
10. A method according to claim 5, further comprising selecting the patch within the region of interest for each image from an aligned stack of patches within the region.
11. A method according to claim 5, wherein the determining of the at least one initial thickness parameter comprises forming estimates of a first and second thickness parameters at the current region of interest based on the set of contrast metrics computed for the set of patches.
12. A method according to claim 5, wherein the determining of the at least one revised thickness parameter comprises analysing the distribution of depth values for the region to
32
obtain current estimates for a top surface location and a bottom surface location of the specimen, the analysing comprising at least one of:
(i) selecting a top surface location from a smallest one of the depth values;
(ii) selecting a bottom surface location from a largest one of the depth values; and
(iii) evaluating a percentile depth value of the distribution as one of the top or bottom surface locations.
13. A method according to claim 12, wherein the determining of the at least one revised thickness parameter comprises forming a correction factor using at least the initial thickness parameter and the current estimates and modifying the current estimates using the correction factor.
14. A method according to claim 13 wherein the initial thickness parameter comprises an initial thickness estimate, and a current thickness estimate comprises a difference of the top surface location and the bottom surface location, and the correction factor is an average of the difference between the initial thickness estimate and the current thickness estimate across the regions of the specimen, and the revised thickness parameter is a revised thickness formed by subtracting the correction factor from the initial thickness estimate.
15. A method according to claim 5, further comprising setting a size of the sub-patches according to a feature size within the specimen.
16. A method according to claim 5, wherein the specimen comprises a stained histology slide.
17. A computer readable storage medium having a program recorded thereon, the program being executable by computerised apparatus to determine at least one thickness parameter of a specimen from a stack of images of the specimen obtained from a microscope at a series of depths, said program comprising:
code for determining, within a region of interest, sets of patches at a plurality of corresponding transverse locations in each image within the stack of images;
code for selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being
33
selected with respect to a best focus defined peak region in a set of contrast metrics computed for the set of patches at the transverse location; and
code for determining at least one thickness parameter for the specimen at the region of interest from at least a distribution of the selected depth values across the plurality of transverse locations of the region of interest.
18. A computer readable storage medium having a program recorded thereon, the program being executable by computerised apparatus to determine at least one thickness parameter of a specimen from a stack of images of the specimen captured at a series of depths, said program comprising:
code for determining, within a region of interest, a patch at a corresponding location in each image within the stack of images to form a set of patches;
code for determining at least one initial thickness parameter of the specimen at the selected region of interest based on a set of contrast metrics computed for the set of patches; code for determining sets of sub-patches at a plurality of corresponding transverse locations within each patch in the set of patches;
code for selecting a depth value associated with a specimen feature located between top and bottom surfaces at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the sub- patches at the transverse location; and
code for determining at least one revised thickness parameter for the specimen at the region of interest from a distribution of the selected depth values across the plurality of transverse locations of the region of interest and the initial thickness parameter.
19. A microscope system comprising:
a microscope having a controllable stage upon which a specimen is positionable; a camera for capturing images of the specimen via the microscope; and
a processor system coupled to the camera for receiving and storing the images and for controlling movement of the stage during image capture, the processor system having a memory with a program recorded thereon, the program being executable by a processor to determine at least one thickness parameter of the specimen from a stack of the images of the specimen captured at a series of depths, said program comprising:
code for determining, within a region of interest, sets of patches at a
34
corresponding transverse locations in each image within the stack of images;
code for selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the set of patches at the transverse location; and
code for determining at least one thickness parameter for the specimen at the region of interest from a distribution of the selected depth values across the plurality of transverse locations of the region of interest.
20. A microscope system comprising:
a microscope having a controllable stage upon which a specimen is positionable; a camera for capturing images of the specimen via the microscope; and
a processor system coupled to the camera for receiving and storing the images and for controlling movement of the stage during image capture, the processor system having a memory with a program recorded thereon, the program being executable by a processor to determine at least one thickness parameter of a specimen from a stack of images of the specimen captured at a series of depths, said program comprising:
code for determining, within a region of interest, a patch at a corresponding location in each image within the stack of images to form a set of patches;
code for determining at least one initial thickness parameter of the specimen at the selected region of interest based on a set of contrast metrics computed for the set of patches;
code for determining sets of sub-patches at a plurality of corresponding transverse locations within each patch in the set of patches;
code for selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the sub-patches at the transverse location; and
code for determining at least one revised thickness parameter for the specimen at the region of interest from a distribution of the selected depth values across the plurality of transverse locations of the region of interest and the initial thickness parameter.
35
21. A method according to claim 1, wherein the at least one thickness parameter is determined independently of a determination of a specimen thickness at any of the transverse locations.
22. A method according to claim 1, wherein the at least one thickness parameter is determined based on a comparison of the selected depth values at at least two of the transverse locations.
36
STATEMENT UNDER ARTICLE 19 (1 )
The invention of the subject application operates to select a single depth value of the best focus at each transverse location across a region of interest. This creates a distribution of depth values across the region of interest within the specimen. The distribution of depth values is then analysed to determine the thickness of the specimen.
The prior art cited into the International Search Report failed to teach the use of a distribution of depth values across a region of interest, as per the currently amended claims, to determine a single thickness parameter. The prior art effectively uses a focus function to determine top and bottom surfaces of the specimen for estimating thickness at a particular transverse location, where this process can be carried out for each transverse location. However, the prior art does not utilise any distribution of depth values across the region of interest.
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| AU2013273789A AU2013273789A1 (en) | 2013-12-20 | 2013-12-20 | Thickness estimation for Microscopy |
| AU2013273789 | 2013-12-20 |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| WO2015089564A1 WO2015089564A1 (en) | 2015-06-25 |
| WO2015089564A4 true WO2015089564A4 (en) | 2015-08-13 |
Family
ID=53401785
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/AU2014/001147 WO2015089564A1 (en) | 2013-12-20 | 2014-12-16 | Thickness estimation for microscopy |
Country Status (2)
| Country | Link |
|---|---|
| AU (1) | AU2013273789A1 (en) |
| WO (1) | WO2015089564A1 (en) |
Families Citing this family (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| JP6522535B2 (en) * | 2016-02-29 | 2019-05-29 | 富士フイルム株式会社 | Cell observation apparatus and method |
| US10341551B1 (en) * | 2018-05-21 | 2019-07-02 | Grundium Oy | Method, an apparatus and a computer program product for focusing |
Family Cites Families (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US7756305B2 (en) * | 2002-01-23 | 2010-07-13 | The Regents Of The University Of California | Fast 3D cytometry for information in tissue engineering |
| WO2005119575A2 (en) * | 2004-05-27 | 2005-12-15 | Aperio Technologies, Inc | Systems and methods for creating and viewing three dimensional virtual slides |
| JP5655557B2 (en) * | 2010-07-12 | 2015-01-21 | ソニー株式会社 | Microscope control device, image display device, image management server, focus position information generation method, image display method, image management method, and microscope image management system |
| US9297995B2 (en) * | 2011-02-11 | 2016-03-29 | University Of South Florida | Automatic stereological analysis of biological tissue including section thickness determination |
| JP5780865B2 (en) * | 2011-07-14 | 2015-09-16 | キヤノン株式会社 | Image processing apparatus, imaging system, and image processing system |
-
2013
- 2013-12-20 AU AU2013273789A patent/AU2013273789A1/en not_active Abandoned
-
2014
- 2014-12-16 WO PCT/AU2014/001147 patent/WO2015089564A1/en active Application Filing
Also Published As
| Publication number | Publication date |
|---|---|
| AU2013273789A1 (en) | 2015-07-09 |
| WO2015089564A1 (en) | 2015-06-25 |
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