Abstract: Apparatus and methods for determining a property of a bodily sample using a microscope are described. A sample carrier includes a plurality of microscopy sample chambers configured to receive a least a portion of the bodily sample, while the sample is imaged by the microscope. Each of the microscopy sample chambers has an upper and a lower surface, and the microscopy sample chambers have respective heights between the upper and lower surfaces that are different from each other. The sample carrier defines a microscopy sample chamber inlet hole, that is fluid communication with all of the microscopy sample chambers, such as to facilitate filling of all of the microscopy sample chambers with the portion of the bodily sample, via the microscopy sample chamber inlet hole. Other applications are also described.

Abstract: Apparatus and methods are described for determining a property of a bodily sample using a microscope and optical-density-measurement apparatus, the apparatus including a sample carrier that includes a plurality of microscopy sample chambers configured to receive a first portion of the sample and to facilitate imaging of the first portion of the sample by the microscope, each of the microscopy sample chambers having an upper and a lower surface, and having respective heights between the upper and lower surfaces that are different from each other. The sample carrier includes at least one optical-density-measurement chamber configured to receive a second portion of the sample, and to facilitate optical density measurements being performed optical-density-measurement apparatus upon the second portion of the sample. Other applications are also described.

Abstract: Apparatus and methods are described including a microscope system configured to acquire first and second images of a blood sample at respective times. A computer processor determines whether, between acquisitions of the first and second images, there was motion of a given entity within the sample, by comparing the first and second images to one another. At least partially in response thereto, the computer processor distinguishes between the given entity being a non-parasitic entity and the given entity being a parasite, and generates an output on the output device, at least partially in response thereto. Other applications are also described.

Abstract: Apparatus and methods are described including a sample carrier (22) configured to carry a portion of a bodily sample, at least a portion of the sample carrier being configured to fluoresce, at least under certain conditions. An optical measurement device (24) performs optical measurements upon the portion of the bodily sample that is housed within the sample carrier (22), and at least partially photobleaches an area within the portion of the sample carrier (22) by causing the area to fluoresce. By detecting that the area within the portion of the sample carrier (22) has been photobleached, an output is generated indicating that at least a portion of the sample carrier (22) is contaminated or that optical measurements cannot be performed on the portion of the sample carrier (22), or the optical measurement device (24) is prevented from performing optical measurements upon a sample portion housed within the given portion of the sample carrier (22).

Abstract: Apparatus and methods are described for use with a digital camera that is configured to acquire images of a bodily sample. Two or more stains are configured to stain the bodily sample. A computer processor drives the digital camera to acquire, for each of a plurality of imaging fields of the bodily sample, two or more digital images, at least one of the images being acquired under brightfield lighting conditions, and at least one of the images being acquired under fluorescent lighting conditions. The computer processor performs image processing on the digital images, by extracting visual classification features from the digital images and analyzing the extracted visual classification features. The computer processor outputs a result of the image processing that includes an indication of one or more entities that are contained within the sample. Other applications are also described.

Abstract: Methods, systems and computer program products relating to digital microscopy are disclosed. A digital microscopy method may comprise capturing a plurality of overlapping images of a sample, wherein the capturing of at least one of the plurality of images is performed while the sample and a focal plane are in relative motion along an optical axis at a speed greater than zero; and processing the plurality of images using a reference criterion to determine a reference relative arrangement of the focal plane and the sample along the optical axis.

Abstract: Apparatus and methods for use with a blood sample are described. The blood sample is stained with Hoechst stain and Acridine Orange stain. A plurality of images of the blood sample are acquired. An object is identified as being a white blood cell candidate. A first stained area, which is stained by the Hoechst stain and which is disposed within the white blood cell candidate, is identified. A second stained area, which is stained by the Acridine Orange stain and which is disposed within the white blood cell candidate, is identified. A white blood cell is detected by determining that structural features of the stained areas satisfy predetermined criteria associated with a white blood cell. Other applications are also described.

Abstract: Disclosed herein, inter alia, is method, kit and systems for detecting a pathogen infection in a bodily sample, the method comprising (i) staining said bodily sample with two or more dyes, comprising at least one dye predominantly staining DNA to thereby provide differential staining between DNA and at least one other cellular component being different from DNA; (ii) identifying at least a first stained area comprising the DNA, if exists in the sample, and at least one other stained area comprising the other cellular component; (iii) extracting structural features for the first stained area and the at least one other stained area, said structural features comprise at least one of (i) size of at least one of the first stained area and one other stained area and (ii) location of said first stained area and said at least one other stained area one with respect to the other; and (iv) determining the presence of a suspected pathogen in the bodily sample if a first stained area was identified and said structural fe

Abstract: Apparatus and methods are described for use with a sample that includes a plurality of red blood cells. A series of images associated with a series of depth levels of the sample are acquired, by performing a depth scan of the 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 sample using the microscope, by identifying that a drop in image contrast occurs at the identified depth level. The 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.

Abstract: Apparatus and methods are described for use with a digital microscope unit that includes a digital microscope. A biological cell sample disposed within a sample carrier, is received into the digital microscope unit. For at least one imaging field of the biological cell sample, it is determined that, within the imaging field, there is a variation in the focal depth of the biological sample with respect to the microscope. At least one image of the imaging field is captured. A characteristic of the biological sample is determined by analyzing the captured image of the imaging field, the analyzing including, in response to determining that there is a variation in the focal depth of the biological sample with respect to the microscope, accounting for the variation in the focal depth of the biological sample with respect to the microscope. Other applications are also described.

Abstract: A digital microscopy method, comprising: obtaining data representative of a series of images of at least a portion of a cell sample, the images being captured by performing a depth scan using a digital microscope, the series of images being associated with a series of depth levels of the cell sample, wherein the portion encompasses a mapping field, and the mapping field comprises a plurality of focus analysis regions; and calculating, using the images, a focus configuration for at least two of the focus analysis regions within the mapping field, giving rise to data indicative of focus variations within the mapping field.

Abstract: Apparatus and methods are described for use with a cell sample. For each of one or more imaging fields of the cell sample, a depth scan of the cell sample is performed using a microscope. One of the depth levels is identified as being an optimum focal plane for imaging one or more entities within the sample using the microscope, at least partially in response to detecting that the depth level corresponds to a drop in image contrast relative to image contrast at other depth levels. Based upon the depth level identified as being the optimum focal plane for each of the one or more imaging fields of the cell sample, a scanning depth interval over which to perform a depth scan of the cell sample at a further imaging field is defined. Other applications are also described.

Abstract: A digital microscopy method, comprising: obtaining data representative of a series of images of at least a portion of a cell sample, the images being captured by performing a depth scan using a digital microscope, the series of images being associated with a series of depth levels of the cell sample, wherein the portion encompasses a mapping field, and the mapping field comprises a plurality of focus analysis regions; and calculating, using the images, a focus configuration for at least two of the focus analysis regions within the mapping field, giving rise to data indicative of focus variations within the mapping field.

Abstract: The present disclosure provides a method of determining a reference depth level within a cell sample. The method comprises obtaining data representative of a series of images captured by performing a depth scan of the cell sample using a digital microscope, the series of images being associated with a series of depth levels of the cell sample; processing said data for detecting at least one depth level corresponding to a drop in image contrast; and identifying the detected depth level as the reference depth level.

Abstract: The invention discloses an apparatus and method for automatic detection of pathogens within a sample. The apparatus and method are especially useful for high-throughput and/or low-cost detection of parasites with minimal need for trained personnel. The invention entails automated microscopic data acquisition, and performing image processing of images captured from a sample using classification algorithms. Visual classification features of structures are extracted from the image and compared to visual classification features associated with known pathogens. A determination is reached whether a pathogen is present in the sample; and if present, the pathogen may be identified to a pathogen species. Diagnosis is rapid and does not require medically trained personnel.

Abstract: Apparatus and methods are described for use with a digital camera that is configured to acquire images of a bodily sample. Two or more stains are configured to stain the bodily sample. A computer processor drives the digital camera to acquire, for each of a plurality of imaging fields of the bodily sample, two or more digital images, at least one of the images being acquired under brightfield lighting conditions, and at least one of the images being acquired under fluorescent lighting conditions. The computer processor performs image processing on the digital images, by extracting visual classification features from the digital images and analyzing the extracted visual classification features. The computer processor outputs a result of the image processing that includes an indication of one or more entities that are contained within the sample. Other applications are also described.

Abstract: Methods, systems and computer program products relating to digital microscopy are disclosed. A digital microscopy method may comprise capturing a plurality of overlapping images of a sample, wherein the capturing of at least one of the plurality of images is performed while the sample and a focal plane are in relative motion along an optical axis at a speed greater than zero; and processing the plurality of images using a reference criterion to determine a reference relative arrangement of the focal plane and the sample along the optical axis.

Abstract: Disclosed herein, inter alia, is method, kit and systems for detecting a pathogen infection in a bodily sample, the method comprising (i) staining said bodily sample with two or more dyes, comprising at least one dye predominantly staining DNA to thereby provide differential staining between DNA and at least one other cellular component being different from DNA; (ii) identifying at least a first stained area comprising the DNA, if exists in the sample, and at least one other stained area comprising the other cellular component; (iii) extracting structural features for the first stained area and the at least one other stained area, said structural features comprise at least one of (i) size of at least one of the first stained area and one other stained area and (ii) location of said first stained area and said at least one other stained area one with respect to the other; and (iv) determining the presence of a suspected pathogen in the bodily sample if a first stained area was identified and said structural fe

Abstract: The present disclosure provides a method of determining a reference depth level within a cell sample. The method comprises obtaining data representative of a series of images captured by performing a depth scan of the cell sample using a digital microscope, the series of images being associated with a series of depth levels of the cell sample; processing said data for detecting at least one depth level corresponding to a drop in image contrast; and identifying the detected depth level as the reference depth level.

Abstract: The invention discloses an apparatus and method for automatic detection of pathogens within a sample. The apparatus and method are especially useful for high-throughput and/or low-cost detection of parasites with minimal need for trained personnel. The invention entails automated microscopic data acquisition, and performing image processing of images captured from a sample using classification algorithms. Visual classification features of structures are extracted from the image and compared to visual classification features associated with known pathogens. A determination is reached whether a pathogen is present in the sample; and if present, the pathogen may be identified to a pathogen species. Diagnosis is rapid and does not require medically trained personnel.