Koninklijke Philips Corporation N.V.

Bas Hulsken

Sjoerd Stallinga

Jelte Peter Vink

Stein Kuiper

Reinhold Wimberger-Friedl

Ruud Vlutters

Anke Pierik

Marinus Bastiaan Van Leeuwen

Cornelius Antonius Hezemans

Sieglinde Neerken

Dirk Leo Joep Vossen

Zeynep Seflek Unay

Erik M H P Van Dijk

Bart E G J Van Meerbergen

Martijn Wolters

Daniel Carl Mueller

Stuart Hamish Shand

Henricus R M Verberne

Bo Joakim Isaksson

Mark W G Ponjee

Cornelius Hezemans

Henricus Verberne

Erik Van Dijk

Zeynep S Unay

Marc W G Ponjee

Bart E G Van Meerbergen

The invention relates to a method and apparatus for fast and efficient image compression and decompression comprising transform coding of image data to generate an image representation using transform coefficients, bit-plane serialization of the image representation using transform coefficients, and for each bitplane optimal prefix encoding of bits in a bitplane sharing local context, run-length encoding of 0 bit sequences in the bitplane and storing the coefficients received after optimal prefix encoding and 0 run length encoding starting with the sign followed by the bits in the order of significance, starting with the most significant bit to the least significant bit in a seektable in a header section.

Method and apparatus for fast and efficient image compression and decompression

The present invention relates to an illustration of an annotation () at a sample slide (). It is the intention for the invention to copy the annotation () provided at a reference slide () to the sample slide (). Typically, a reference image () of the reference slide () is provided, in particular by scanning the reference slide (). The reference image () therefore has the information about a reference slice () which is carried by the reference slide (). Furthermore, the reference slide () has been marked with a region of interest () and the annotation (), which can be associated with the region of interest (). If such reference slide () is scanned, the respective reference image () comprises the information about the marked region of interest () as well as the annotation (), too. Furthermore, the sample slide () carrying a sample slice () can be scanned, in order to provide a sample image (). The sample slice () and the reference slice () are cut from the same object () of a biological material. In particular, the sample slice () has been cut directly after a cut of a material block has been preformed to provide the reference slice (). Since the reference slice () and the sample slice () are from the same object (), their features are very likely that the reference image () and the sample image () are very similar. Due to this similarity, the annotation () of the reference slide () is copied on a basis of an image recognition between reference image () and the sample image () to the sample slide ().

Information transformation in digital pathology

The present invention relates to a system for generating a synthetic 2D image with an enhanced depth of field of a biological sample. It is described to acquire () with a microscope-scanner () first image data at a first lateral position of the biological sample and second image data at a second lateral position of the biological sample. The microscope-scanner is used to acquire () third image data at the first lateral position and fourth image data at the second lateral position, wherein the third image data is acquired at a depth that is different than that for the first image data and the fourth image data is acquired at a depth that is different than that for the second image data. First working image data is generated () for the first lateral position, the generation comprising processing the first image data and the third image data by a focus stacking algorithm. Second working image data is generated () for the second lateral position, the generation comprising processing the second image data and the fourth image data by the focus stacking algorithm. The first working image data and the second working image data are combined (), during acquisition of image data, to generate the synthetic 2D image with an enhanced depth of field of the biological sample.

System for generating a synthetic 2D image with an enhanced depth of field of a biological sample

The present invention relates to the field of digital pathology and in particular to whole slide scanners. Autofocus imaging can be performed by sampling a first number of pixels of a primary image sensor which is a time delay integration (TDI) sensor, and sampling a second number of pixels of an autofocus image sensor, wherein the second number is between one quarter and three quarters of the first number. Thus, continuous autofocus for rapid light scanning may be provided based on an additional image sensor that is tilted with respect to the optical axis.

Autofocus imaging

The present invention relates to the field of digital pathology and in particular to whole slide scanners. Autofocus imaging can be performed by sampling a first number of pixels of an image sensor and sampling a second number of pixels of the image sensor, wherein the second number is between one quarter and three quarters of the first number. Thus, continuous autofocus for rapid light scanning may be provided using data from a single sensor based on sampling data along a tilt with respect to the optical axis.

This invention pertains to a method for microscopically imaging a sample, with a digital scanner comprising a sensor including a 2D array of pixels and to a digital scanning microscope carrying out this method. It is notably provided a method for microscopically imaging a sample with a scanner comprising a sensor including a 2D array of pixels in an XY coordinate system, the axis Y being substantially perpendicular to the scan direction, wherein the scanner is arranged such that the sensor can image an oblique cross section of the sample, and wherein the method comprises the steps of: &#x2022; activating a first sub-array of the 2D array of pixels, the first sub-array extending mainly along the Y axis at a first X coordinate (X), &#x2022; creating a first image by imaging a first area of the sample by means of the first sub-array of pixels. According to aspects of the invention, it is further proposed a scanner carryout this method and using the same 2D array sensor for imaging and auto-focusing purpose.

Sensor for microscopy

An imaging sensor comprising a 2D array of pixels in an XY coordinate system with gaps for electronic circuitry is presented. Furthermore, a scanning imaging system for imaging an oblique cross section of a sample with such a sensor is provided. Especially when the imaging sensor is in a tilted configuration this sensor is of specific advantages. The sensor allows for maximizing the photoactive part of the pixels in the photosensitive area of the sensor which leads to a maximized the fill factor. Furthermore this leads to a very light sensitive sensor and hence microlenses can be avoided. The gap or gaps of the imaging sensor facilitate also a faster read out because more circuitry can be positioned on the imaging sensor within the gap.

Scanning imaging system with a novel imaging sensor with gaps for electronic circuitry

A novel method is disclosed to allow for the simultaneous capture of image data from multiple depths of a volumetric sample. The method allows for the seamless acquisition of a 2D or 3D image, while changing on the fly the acquisition depth in the sample. This method can also be used for auto focusing. Additionally this method of capturing image data from the sample allows for optimal efficiency in terms of speed, and light sensitivity, especially for the herein mentioned purpose of 2D or 3D imaging of samples when using a tilted configuration as depicted in FIG.. The method may be particularly used with an imaging sensor comprising a 2D array of pixels in an orthogonal XY coordinate system where gaps for electronic circuitry are present. Also other imaging sensor may be used. Further, an imaging device is presented which automatically carries out the method.

Method for simultaneous capture of image data at multiple depths of a sample

The present invention relates to the field of digital pathology and in particular to whole slide scanners. Autofocus imaging can be performed by sampling a first number of pixels of a primary image sensor and sampling a second number of pixels of an autofocus image sensor, wherein the second number is between one quarter and three quarters of the first number. Thus, continuous autofocus for rapid light scanning may be provided based on an additional image sensor that is tilted with respect to the optical axis.

Autofocus imaging for a microscope

The present invention relates to the field of digital pathology and in particular to whole slide scanners. A tilted autofocus image sensor images an oblique cross-section of the slide. For focusing multiple sequential overlapping images, which have been taken by the tilted sensor, are compared. The axial position of the tissue layer can be determined from the polar error signal resulting from this differential measurement.

Autofocus based on differential measurements

A scanning microscope includes a stage for holding a sample, a scan mechanism, a probing system for probing a region of the sample, a position sensor, and a controller. The scan mechanism is configured to translate the stage between at least two axial positions. The probing system includes an optical element and a photosensor having a readout region, where the readout region extends in a direction which is transverse to an ideal orientation of the stage. The position sensor is configured to measure a transverse position of the stage and/or of an orientation of the stage. The controller is configured to adapt the probing system as a function of the measured transverse position and/or the measured orientation.

Scanning microscope

An autofocus imaging system for a microscope system includes a tilted autofocus image sensor that images an oblique cross-section of a slide. The autofocus imaging system focuses multiple sequential overlapping images, which have been taken by the tilted autofocus image sensor, by making a comparison of the multiple sequential overlapping images. An axial position of a tissue layer on the slide can be determined from a polar error signal resulting from this comparison.

Determining a polar error signal of a focus position of an autofocus imaging system

A method of analyzing a sample fluid containing organic microobjects is proposed. The method comprises the steps of: up-concentrating (S) the microobjects by removing, in a total time T, a volume Vof the sample fluid from the upconcentrate sample microobjects; immersing (S) the microobjects in a transfer fluid, or leaving the microobjects in a remaining portion of the sample fluid, the remaining portion of the sample fluid then providing the transfer fluid; filtering (S), in a total time T, a volume Vof the transfer fluid by a filter, thereby accumulating the microobjects on the filter; and generating (S) an image of the microobjects accumulated on the filter; wherein the throughput V/Tof the step of up-concentrating (S) is greater than the throughput V/T, of the step of filtering (S). The filter may be a second filter, and the step of up-concentrating (S) may involve: filtering the sample fluid by a first filter, thereby accumulating the microobjects on the first filter. An apparatus or system for analyzing a sample fluid containing organic microobjects is also disclosed.

Up-concentration of organic microobjects for microscopic imaging

The invention pertains to the field of image processing in digital pathology. It notably proposes a method for processing a first digital image, representing a sample in a region, and which image has been acquired from the sample by means of a microscopic imaging system () and is stored in a multi-resolution image data structure (), comprising the steps of:&#x2014;retrieving () a sub-region of the first digital image at a first resolution, &#x2014;executing () a transform function on the retrieved sub-region, the transform function modifying a content of the sub-region according to at least one metric derived from a second resolution representation of the first digital image.

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Eindhoven, Netherlands

Bas Hulsken