Abstract: A method for matching a three-dimensional first image of at least one discrete entity with a three-dimensional second image of the at least one discrete entity is provided. The at least one discrete entity includes a biological sample and a plurality of constituent parts of a marker. The method includes: generating a first representation of the marker from the first image; generating a second representation of the marker from the second image; and based upon the representations matching, matching the first image with the second image; or based upon the representations not matching, rejecting the match. Generating the representations includes determining vectors from at least one reference item to at least some of the constituent parts of the marker, determining for the vectors at least one value of a property, and generating the representations of the marker based on a frequency of the at least one value of the property.

Abstract: A method for determining a calibration of a microscope includes illuminating a first region of a reference object using illumination light, the reference object including multiple pattern elements arranged in a known regular pattern, the first region including a first pattern element, generating a first image of the first region, generating first image data corresponding to the first image, determining an approximate position of a second pattern element based on the first image data and the known regular pattern, determining a second region of the reference object including the a second pattern element based on the approximate position, illuminating the second region of the reference object using the illumination light, generating a second image of the second region, generating second image data corresponding to the second image, and determining parameters of the calibration for the microscope based on the first image data and the second image data.

Abstract: A method for improving signal-to-noise of image frames is provided. The method includes estimating a representative velocity of an optical flow in an image frame sequence. The method also includes determining an interpolation factor from the representative velocity of the optical flow. The method also includes employing a trained artificial neural network for generating an expanded image frame sequence. The expanded image frame sequence includes a number of interpolating image frames. Each interpolating image frame interpolates between subsequent image frames of the image frame sequence. The number of interpolating image frames corresponds to the interpolation factor. The method also includes computing a time-dependent combination of image frames from the expanded image frame sequence to generate an output image frame sequence.

Abstract: An image scanning microscope includes an excitation unit that generates excitation light according to an excitation modality, and an objective lens directed at a sample space to direct the excitation light and to receive the detection light. A scanning unit of the image scanning microscope is arranged along a beam path between the excitation unit and the objective lens to selectively direct the excitation light. The image scanning microscope includes a detection arrangement including a spectral encoding element to change the spatial distribution of the intensity of the detection light and an array detector. A main beam splitter of the image scanning microscope directs the excitation light into the objective lens, and directs the detection light. The image scanning microscope includes a control unit to control the excitation unit to set the excitation modality, and to determine a spatial distribution of a concentration of two different fluorophore species.

Abstract: A detection arrangement for an optical scanning microscope includes a first beam path comprising a first array detector, and an acousto-optical device configured to receive descanned detection light, and to direct a first part of the detection light into the first beam path. The first part of the detection light includes at least one selected wavelength range determined by at least one frequency of acoustic waves generated by a transducer of the acousto-optical device. The detection arrangement further includes a controller configured to control the transducer of the acousto-optical device for determining the at least one selected wavelength range.

Abstract: A data processing apparatus for processing a digital input image is configured to receive the digital input image. The digital input image includes input photon arrival-time data at input image locations. The data processing apparatus is further configured to compute a digital output image based on the digital input image by deconvolution. The digital output image includes output photon arrival-time data at output image locations. The output photon arrival-time data represent an estimate of an unblurred ground-truth of the input photon arrival-time data. The data processing apparatus is further configured to compute the deconvolution by an iterative algorithm using an update function. The update function depends on a point-spread function, a previous estimate of the ground-truth, and the input photon arrival-time data.

Abstract: A computer-implemented method for computing an estimate of a first signal of a plurality of signals is provided. The plurality of signals is contained in a digital color input image. Each signal has a different ground truth spectrum. The digital color input image includes a plurality of pixels. The method includes extracting a subset from the plurality of pixels, extracting from the subset by spectral unmixing a preliminary estimate of the first signal as a first unmixed signal, and a preliminary estimate of at least one further signal of the plurality of signals as at least one further unmixed signal, computing from the subset an estimate of a dependency of the first unmixed signal on the at least one further signal as a crosstalk quantity for the subset, and removing the crosstalk quantity from the first unmixed signal to obtain the estimate of the first signal for the subset.

Abstract: A multi-core processor system includes a plurality of processors, a first global buffer, and a second global buffer. The multi-core processor system distributes a kernel to the plurality of processors for concurrently executing a plurality of threads of the kernel by each processor. While each thread of the kernel is concurrently executed, processing steps defined within the kernel are iteratively performed. The processing steps include (i) computing a forward transform of intermediary input image data, received from the first global buffer, and providing the forward transformed data to the shared memory, (ii) processing the forward transformed data to provide the processed data to the shared memory, (iii) computing a backward transform of the processed data and providing the backward transformed data to the second global buffer, and (iv) synchronizing the first global buffer between the plurality of processors before the first global buffer provides the intermediary input image data.

Abstract: A signal processing apparatus for enhancing a digital input signal (I(xi)) recorded by a recording system having a system response (H(xi)), is configured to retrieve the digital input signal (I(xi)) and compute a baseline estimate (ƒ(xi)) of the digital input signal, the baseline estimate representing a baseline of the digital input signal and comprising features of the digital input signal that are larger than a feature length (fl). The apparatus is further configured to remove the baseline estimate from the digital input signal to obtain an output signal comprising spatial features that are smaller than the feature length, retrieve a characteristic length (cl) of the system response (H(xi)) and compute the baseline estimate (ƒ(xi)) using a feature length that is smaller than the characteristic length of the system response (H(xi)).

Abstract: An apparatus for enhancing an input phase distribution (I(xi)) is configured to retrieve the input phase distribution (I(xi)) and compute a baseline estimate (ƒ(xi)) as an estimate of a baseline (I2 (xi)) in the input phase distribution (I(xi)). The apparatus is further configured to obtain an output phase distribution (O(xi)) based on the baseline estimate (ƒ(xi)) and the input phase distribution (I(xi)).

Abstract: The invention relates to a data processing device for an imaging apparatus, the device being configured to obtain a length threshold value, to access input image data representing at least one digital input image, wherein the input image data comprise a shading signal representing a brightness decrease towards the edges of the at least one digital input image, and a content signal representing image features of the at least one digital input image, the image features having a length that is smaller than the length threshold value, to compute a baseline image based on the input image data and the length threshold value, wherein the baseline image is representative of an estimate of the shading signal, to generate at least one digital output image representative of an estimate of the content signal by at least one of a) subtracting the baseline image from the input image data and b) dividing the input image data by the baseline image.

Abstract: A data processing apparatus for processing a digital input image is configured to receive the digital input image. The digital input image includes input photon arrival-time data at input image locations. The data processing apparatus is further configured to compute a digital output image based on the digital input image by deconvolution. The digital output image includes output photon arrival-time data at output image locations. The output photon arrival-time data represent an estimate of an unblurred ground-truth of the input photon arrival-time data. The data processing apparatus is further configured to compute the deconvolution by an iterative algorithm using an update function. The update function depends on a point-spread function, a previous estimate of the ground-truth, and the input photon arrival-time data.

Abstract: A marker for marking a predetermined structure within a biological sample includes a marker base having an affinity reagent, and an attachment structure connected to the affinity reagent having two attachment sites. The attachment structure includes a cleavage site arranged between the attachment sites. The attachment structure is capable of being cut at the cleavage site by a cleaving agent in order to remove an attachment site from the marker base. The marker further includes at least two reporters. Each reporter includes a linker structure having a complementary attachment site configured to attach to one of the attachment sites, and a combination of at least two different fluorescent dyes. The combination of the at least two different fluorescent dyes is unique for each reporter. The complementary attachment site is unique for each reporter and configured such that each reporter attaches to a different attachment site of the marker base.

Abstract: A method for estimating baseline in a signal, the signal being represented by input signal data (I(xi)), includes estimating a baseline contribution (I2(xi)) in the signal to obtain baseline estimation data (f(xi)), wherein the baseline estimation data (f(xi)) are computed as a fit to at least a subset of the input signal data (I(xi)) by minimizing a least-square minimization criterion (M(f(xi))). Deblurred output signal data (O(xi)) are obtained based on the baseline estimation data (f(xi)) and the input signal data (I(xi)). The least-square minimization criterion (M(f(xi))) comprises a penalty term (P(f(xi))).

Abstract: A method for analysing a biological sample with analytes includes determining information about the biological sample and the analytes. The analytes are marked by a plurality of markers. The method further includes generating a probabilistic model of a distribution of the analytes within the biological sample based on the determined information, generating at least one optical readout of the biological sample, and determining presence of at least one analyte in the at least one optical readout based at least partially on the probabilistic model of the distribution of the analytes within the biological sample.

Abstract: A method for estimating a stimulated emission depletion microscopy (STED) resolution includes generating a first frame representing a reference image from a field-of-view, the reference image having a predetermined reference resolution, and generating at least one second frame representing a STED image from the same field-of-view, the STED image having the STED resolution to be estimated. The at least one second frame is blurred by applying a convolution kernel with at least one fit parameter to the second frame. An optimal value of the at least one fit parameter of the convolution kernel is determined for which a difference between the first frame and the blurred at least one second frame is minimized. The STED resolution is estimated based on the optimal value of the at least one fit parameter and the predetermined reference resolution.

Abstract: A method for improving signal-to-noise of image frames is provided. The method includes estimating a representative velocity of an optical flow in an image frame sequence. The method also includes determining an interpolation factor from the representative velocity of the optical flow. The method also includes employing a trained artificial neural network for generating an expanded image frame sequence. The expanded image frame sequence includes a number of interpolating image frames. Each interpolating image frame interpolates between subsequent image frames of the image frame sequence. The number of interpolating image frames corresponds to the interpolation factor. The method also includes computing a time-dependent combination of image frames from the expanded image frame sequence to generate an output image frame sequence.

Abstract: A digital image processing apparatus for computing a baseline estimate of a digital input image is provided. The digital image processing apparatus is configured to obtain a digital intermediate image by downsampling the digital input image by a predetermined downsampling factor, and compute the baseline estimate based on the digital intermediate image.

Abstract: A method for matching a three-dimensional first image of at least one discrete entity with a three-dimensional second image of the at least one discrete entity is provided. The at least one discrete entity includes a biological sample and a plurality of constituent parts of a marker. The method includes: generating a first representation of the marker from the first image; generating a second representation of the marker from the second image; and based upon the representations matching, matching the first image with the second image; or based upon the representations not matching, rejecting the match. Generating the representations includes determining vectors from at least one reference item to at least some of the constituent parts of the marker, determining for the vectors at least one value of a property, and generating the representations of the marker based on a frequency of the at least one value of the property.

Abstract: An apparatus for baseline estimation in input signal data is configured to retrieve input signal data (I(xi)) and to subtract baseline estimation data (ƒ(xi)) from the input signal data (I(xi)) to compute output signal data. The apparatus is further configured to compute the baseline estimation data (ƒ(xi)) from a convolution using a discrete Green's function (G(xi)).