Method and system for imaging a cell sample
Apparatus and methods are described for use with a cell sample that includes a plurality of cells disposed in a monolayer. A series of images associated with a series of depth levels of the cell sample are acquired, by performing a depth scan of cell sample with a microscope. One of the depth levels is identified as being an optimum focal plane for imaging one or more entities within the cell sample using the microscope, by identifying that a drop in image contrast occurs at the identified depth level relative to the image contrast of images acquired at depth levels within a given range of distances from the identified depth level. The cell sample is imaged using the microscope, by focusing the microscope at an investigative depth level that is based on the identified depth level. Other applications are also described.
1. A method for use with a cell sample that includes a plurality of cells disposed in a monolayer, the method comprising:
acquiring a series of images associated with a series of depth levels of the cell sample, by performing a depth scan of cell sample with a microscope;
determining image contrast for the images acquired at at least some of the depth levels;
identifying one of the depth levels as being an optimum focal plane for imaging one or more entities within the cell sample using the microscope, by identifying that a drop in image contrast occurs at the identified depth level relative to the image contrast of images acquired at depth levels within a given range of distances from the identified depth level; and
imaging the cell sample using the microscope, by focusing the microscope at an investigative depth level that is based on the identified depth level.
2. The method according to claim 1 , wherein identifying one of the depth levels as the optimum focal plane comprises identifying that the identified depth level is such that image contrast at the identified depth level is lower than image contrast associated with a depth level immediately preceding the identified depth level in the series of depth levels and lower than image contrast associated with a depth level immediately following the identified depth level in the series of depth levels.
3. The method according to claim 1 , wherein detecting that the drop in image contrast occurs at the identified depth level comprises computing, for each image, a contrast related value that enables derivation of an image contrast for each image.
4. The method according to claim 1 , wherein acquiring the series of images associated with the series of depth levels of the cell sample comprises performing a depth scan of the cell sample, with the microscope, the depth scan spanning between 5 and 1000 micrometers.
5. The method according to claim 1 , wherein acquiring the series of images associated with the series of depth levels of the cell sample comprises performing a depth scan of the cell sample, with the microscope, the depth scan spanning less than 50 micrometers.
6. The method according to claim 1 , further comprising determining an estimated optimum focal plane, wherein acquiring the series of images associated with the series of depth levels of the cell sample comprises performing a depth scan of the cell sample, with the microscope, the depth scan covering the estimated optimum focal plane.
7. The method according to claim 1 , wherein identifying one of the depth levels as the optimum focal plane comprises:
determining a variance deepness value associated with the depth level, the variance deepness value being a function of a variance-related value of the depth level, and a maximum of variance-related values associated with depth levels that are within the given range of distances from the depth level, and
identifying the depth level as being the optimum focal plane at least partially based upon the variance deepness value associated with the depth level.
8. The method according to claim 1 , wherein the method is for use with a cell sample having predominantly red blood cells, and identifying one of the depth levels as being an optimum focal plane comprises identifying one of the depth levels as being an optimum focal plane for imaging one or more entities within the cell sample having predominantly red blood cells using the microscope.
9. The method according to claim 1 , wherein focusing the microscope at the investigative depth level further comprises shifting a focus plane of the microscope from the identified depth level by a predetermined value.
10. The method according to claim 1 , wherein identifying that the drop in image contrast occurs at the identified depth level comprises calculating image contrast using a contrast function selected from the group consisting of: variance, standard deviation, and sum of absolute-value of derivatives.
11. The method according to claim 1 , further comprising, prior to acquiring the series of images, allowing the cell sample to form the monolayer.
12. The method according to claim 11 , wherein allowing the sample to form the monolayer comprises:
introducing the cell sample into a carrier that is a closed cavity that includes a base surface; and
allowing the cells to settle on the base surface of the carrier to form a monolayer of cells on the base surface of the carrier.
13. The method according to claim 11 , wherein allowing the cell sample to form the monolayer comprises allowing at least 80% of the cells to have direct contact with the base surface of the carrier.
14. The method according to claim 1 , further comprising acquiring an additional series of images associated with an additional series of depth levels, wherein a scanning depth interval of the additional series of images is wider than a scanning depth interval of the series of images.
15. The method according to claim 14 , wherein acquiring the additional series of images associated with the additional series of depth levels comprises acquiring the additional series of images associated with the additional series of depth levels in response to a deepness of the drop in image contrast at the identified depth level being below a predetermined deepness threshold.
16. The method according to claim 1 , wherein:
performing the depth scan of the cell sample with the microscope comprises performing the depth scan of the cell sample using the microscope, under a first illumination condition;
identifying one of the depth levels as being the optimum focal plane for imaging the one or more entities within the cell sample using the microscope comprises identifying one of the depth levels as being an optimum focal plane for imaging the one or more entities within the cell sample using the microscope, under the first illumination condition; and
imaging the cell sample using the microscope comprises imaging the cell sample under a second illumination condition that is different from the first illumination condition, using the microscope, by focusing the microscope at an investigative depth level that is based on the identified depth level.
17. The method according to claim 16 , wherein focusing the microscope at the investigative depth level that is based on the identified depth level further comprises shifting a focus plane of the microscope from the identified depth level by a predetermined value.
18. The method according to claim 16 , wherein:
performing the depth scan of the cell sample using the microscope, under the first illumination condition comprises performing a depth scan of the cell sample using the microscope, under brightfield illumination conditions;
identifying one of the depth levels as being the optimum focal plane for imaging the one or more entities within the cell sample using the microscope comprises identifying one of the depth levels as being an optimum focal plane for imaging the one or more entities within the cell sample using the microscope, under the brightfield illumination conditions; and
imaging the cell sample using the microscope comprises imaging the cell sample under fluorescent lighting conditions, using the microscope, by focusing the microscope at an investigative depth level that is based on the identified depth level.
19. Apparatus for use with a cell sample that includes a plurality of cells disposed in a monolayer, the apparatus comprising:
a microscope, configured to acquire a series of images associated with a series of depth levels of the cell sample, by performing a depth scan of the cell sample; and
a computer processor comprising an autofocus computation module configured to:
receive the series of images from the microscope;
determine image contrast for the images acquired at at least some of the depth levels;
identify one of the depth levels as being an optimum focal plane for imaging one or more entities within the cell sample using the microscope, by identifying that a drop in image contrast occurs at the identified depth level relative to the image contrast of images acquired at depth levels within a given range of distances from the identified depth level; and
command the microscope to acquire an investigative image of the cell sample while the focus plane of the microscope is set at an investigative depth level that is based upon the identified depth level.
20. The apparatus according to claim 19 , wherein the autofocus computation module is configured to command the microscope to set the focus plane at an investigative depth level at which a focus plane of the microscope is shifted from the identified depth level by a predetermined value.
21. The apparatus according to claim 19 , wherein the autofocus computation module is configured to identify that the drop in image contrast occurs at the identified depth level by calculating image contrast using a contrast function selected from the group consisting of: variance, standard deviation, and sum of absolute-value of derivatives.
22. The apparatus according to claim 19 , wherein:
the microscope is configured to perform the depth scan of the cell sample by performing the depth scan of the cell sample, under a first illumination condition;
the autofocus computation module is configured to identify one of the depth levels as being the optimum focal plane for imaging the one or more entities within the cell sample using the microscope by identifying one of the depth levels as being an optimum focal plane for imaging the one or more entities within the cell sample using the microscope, under the first illumination condition; and
the computer processor is configured to command the microscope to acquire the investigative image of the cell sample under a second illumination condition that is different from the first illumination condition, while the focus plane of the microscope is set at the investigative depth level that is based on the identified depth level.
23. The apparatus according to claim 19 , wherein:
the microscope is configured to perform the depth scan of the cell sample by performing the depth scan of the cell sample, under brightfield illumination conditions;
the autofocus computation module is configured to identify one of the depth levels as being the optimum focal plane for imaging the one or more entities within the cell sample using the microscope by identifying one of the depth levels as being an optimum focal plane for imaging the one or more entities within the cell sample using the microscope, under the brightfield illumination conditions; and
the computer processor is configured to command the microscope to acquire the investigative image of the cell sample under fluorescent lighting conditions, while the focus plane of the microscope is set at the investigative depth level that is based on the identified depth level.
24. The apparatus according to claim 19 , wherein the apparatus is for use with a cell sample having predominantly red blood cells, and the computer processor is configured to identify one of the depth levels as being an optimum focal plane for imaging one or more entities within the cell sample having predominantly red blood cells using the microscope.
25. The apparatus according to claim 19 , further comprising a carrier that is a closed cavity that includes a base surface and that is configured to receive the cell sample, wherein the microscope is configured to acquire the series of images associated with a series of depth levels of the cell sample when the plurality of cell have formed a monolayer in which at least 80% of the cells have direct contact with the base surface of the carrier.