Abstract: A method for retrieving a target position in a microscopic sample using position retrieval information, the position retrieval information including a set of geometric descriptors describing a spatial relation between a target position identifier and a plurality of reference position identifiers corresponding to positions of a plurality of reference markers.

Abstract: A method for providing position information for retrieving a target position in a microscopic sample includes providing a first representation of the sample at a first resolution including the target position; specifying a first target position identifier indicating the target position at the first resolution; acquiring an image stack comprising the target position indicated by the first target position identifier; providing a second representation at a second resolution higher than the first resolution based on the image stack; specifying a second target position identifier indicating the target position at the second resolution; specifying a plurality of reference position identifiers in the second representation indicating positions of optically detectable reference markers at the second resolution; and determining a set of geometric descriptors describing spatial relations between the second target position identifier and the plurality of reference position identifiers to provide the position information.

Abstract: A processor for lifetime-based unmixing in fluorescence microscopy is configured to acquire an image having a plurality of pixels, each pixel providing information on photon count and photon arrival times, generate a phasor plot that is a vector space representation of the image, partition the image into image segments, evaluate the image segments according to total photon counts of the corresponding subsets of pixels, and execute a lifetime classification by selecting an image segment having a largest total photon count, determining a region of interest in the image encompassing the image segment, determining a phasor subset in the phasor plot corresponding to the region of interest, and generating a lifetime class including a set of image segments corresponding to the phasor subset. A plurality of lifetime classes is generated by iteratively executing the lifetime classification. The processor is configured to perform lifetime-based unmixing using the life-time classes.

Abstract: A method for preparing for microscopy imaging includes acquiring a plurality of images by a microscopy system and annotating each of the plurality of images with respective metadata concerning the microscopy system. The plurality of images are grouped such that images of the plurality of images at least partially sharing the metadata are grouped in a same group of images.

Abstract: An apparatus is configured to count N-photon events within a time-dependent sequence of events of interactions of a plurality of photons with a light sensitive detector. The apparatus includes a signal-processing device and the light sensitive detector. An N-photon event represents an occurrence of at least N timely overlapping single photon events. The light sensitive detector is adapted to generate a time-dependent digital signal comprising digital patterns representing the time-dependent sequence of events from the detection of the plurality of photons with the light sensitive detector. Each digital pattern in the digital signal comprises a digital pattern width having a continuous sequence of digital values representing at least one event of interaction of at least one photon with the light sensitive detector. The signal-processing device is adapted to identify N-photon events from the digital patterns in the digital signal in dependence from the respective digital pattern width.

Abstract: Spectral information of fluorophores in stained samples is determined by selecting a set of fluorophores, and preparing a set of samples to include one or more fluorophores from the set of fluorophores. A first image for each of the prepared samples is acquired based on excitation of the fluorophores included by the respective sample, and a second image for each of the prepared samples is acquired based on excitation of the fluorophores of all samples and/or of the set of fluorophores. The spectral information is determined based on the two images for one or more predefined spectral channels.

Abstract: A device for unmixing images of samples with fluorescent dyes includes one or more hardware processors. The device is configured to obtain a mixed image of a sample; determine an unmixed image based on the mixed image; determine a noise-map image based on the mixed image; determine a signal-to-noise image based on the unmixed image and the noise map-image; determine a denoised signal-to-noise image based on the signal-to-noise image; and determine a noise-reduced unmixed image of the sample based on the denoised signal-to-noise image and on the noise-map image.

Abstract: A device for an optical imaging system includes a data processing circuit and a memory. The data processing circuit is configured to receive sensor data indicative of a reference image, receive trigger data indicative of a trigger event for determining a drift of the optical imaging system, control recording a drift image triggered by the trigger event, receive further sensor data indicative of the drift image, determine a pixel offset between the reference image and the drift image, determine correction data for correcting the pixel offset based on the pixel offset and send the correction data to correct the pixel offset.

Abstract: A computer-implemented method for compression of Time Tagged data including Time Tagged data records includes the step of separating the Time Tagged data records into a plurality of groups. The method also includes sorting the Time Tagged data records in at least one of the groups by a photon arrival time. The method also includes subtracting a content of a record by a content of an adjacent record resulting in modified records. The method also includes compressing the modified records with a compression method.

Abstract: The present invention relates to a method for generating a result image. The method comprises the steps of: acquiring a STED image of a sample, the STED image comprising pixels; calculating Fourier coefficients of arrival times for the pixels of the image, resulting in real coefficients representing a first image and in imaginary coefficients representing a second image; deriving an intensity image from the STED image; applying a spatial filter to the first image, the second image and the intensity image, resulting in a filtered first image, a filtered second image, and filtered intensity image, respectively; calculating an image G based on the filtered first image and the filtered intensity image; calculating an image S based on the filtered second image and the filtered intensity image; and calculating a result image based on the image G and the image S.

Abstract: A method for providing position information for retrieving a target position in a microscopic sample includes providing a first representation of the sample at a first resolution including the target position; specifying a first target position identifier indicating the target position at the first resolution; acquiring an image stack comprising the target position indicated by the first target position identifier; providing a second representation at a second resolution higher than the first resolution based on the image stack; specifying a second target position identifier indicating the target position at the second resolution; specifying a plurality of reference position identifiers in the second representation indicating positions of optically detectable reference markers at the second resolution; and determining a set of geometric descriptors describing spatial relations between the second target position identifier and the plurality of reference position identifiers to provide the position information.

Abstract: A processor for lifetime-based unmixing in fluorescence microscopy is configured to acquire an image having a plurality of pixels, each pixel providing information on photon count and photon arrival times, generate a phasor plot that is a vector space representation of the image, partition the image into image segments, evaluate the image segments according to total photon counts of the corresponding subsets of pixels, and execute a lifetime classification by selecting an image segment having a largest total photon count, determining a region of interest in the image encompassing the image segment, determining a phasor subset in the phasor plot corresponding to the region of interest, and generating a lifetime class including a set of image segments corresponding to the phasor subset. A plurality of lifetime classes is generated by iteratively executing the lifetime classification. The processor is configured to perform lifetime-based unmixing using the life-time classes.

Abstract: A controller for a microtome configured to cut slices from a sample block is configured to control a display to visualize a virtual representation of the sample block, receive first user input data indicative of a front surface of the sample block, determine a virtual front surface of the sample block based on the first user input data, receive second user input data indicative of an edge of the front surface of the sample block, determine a virtual edge of the front surface of the sample block based on the second user input data, receive third user input data indicative of a cutting plane intersecting the sample block, determine a virtual cutting plane intersecting the sample block based on the third user input, and determine alignment parameters based on the virtual front surface and the virtual edge of the front surface of the sample block and the virtual cutting plane.

Abstract: A computer-implemented method for compression of Time Tagged data including Time Tagged data records includes the step of separating the Time Tagged data records into a plurality of groups. The method also includes sorting the Time Tagged data records in at least one of the groups by a photon arrival time. The method also includes subtracting a content of a record by a content of an adjacent record resulting in modified records. The method also includes compressing the modified records with a compression method.

Abstract: An apparatus is configured to count N-photon events within a time-dependent sequence of events of interactions of a plurality of photons with a light sensitive detector. The apparatus includes a signal-processing device and the light sensitive detector. An N-photon event represents an occurrence of at least N timely overlapping single photon events. The light sensitive detector is adapted to generate a time-dependent digital signal comprising digital patterns representing the time-dependent sequence of events from the detection of the plurality of photons with the light sensitive detector. Each digital pattern in the digital signal comprises a digital pattern width having a continuous sequence of digital values representing at least one event of interaction of at least one photon with the light sensitive detector. The signal-processing device is adapted to identify N-photon events from the digital patterns in the digital signal in dependence from the respective digital pattern width.

Abstract: The present invention relates to a method for generating a result image. The method comprises the steps of: acquiring a STED image of a sample, the STED image comprising pixels; calculating Fourier coefficients of arrival times for the pixels of the image, resulting in real coefficients representing a first image and in imaginary coefficients representing a second image; deriving an intensity image from the STED image; applying a spatial filter to the first image, the second image and the intensity image, resulting in a filtered first image, a filtered second image, and filtered intensity image, respectively; calculating an image G based on the filtered first image and the filtered intensity image; calculating an image S based on the filtered second image and the filtered intensity image; and calculating a result image based on the image G and the image S.

Abstract: A fluorescence-lifetime imaging microscopy method with time-correlated single-photon counting includes using excitation light pulses separated in each case by a measurement interval to excite a sample to emit fluorescence photons. A detector signal that represents the captured fluorescence photons is generated. Detection times are determined based on the detector signal. Imaging is performed based on the detection times. The detection times of all captured fluorescence photons are compiled in a first data memory, common to a plurality of image pixels. The detection times of only those fluorescence photons which were captured in a predetermined number within the respective measurement intervals are compiled in a second data memory, common to the same plurality of image pixels. The detection times compiled in the data memories are combined within a calculation step. The results of the calculation step are stored in a third data memory.

Abstract: A fluorescence-lifetime imaging microscopy method with time-correlated single-photon counting includes using excitation light pulses separated in each case by a measurement interval to excite a sample to emit fluorescence photons. A detector signal that represents the captured fluorescence photons is generated. Detection times are determined based on the detector signal. Imaging is performed based on the detection times. The detection times of all captured fluorescence photons are compiled in a first data memory, common to a plurality of image pixels. The detection times of only those fluorescence photons which were captured in a predetermined number within the respective measurement intervals are compiled in a second data memory, common to the same plurality of image pixels. The detection times compiled in the data memories are combined within a calculation step. The results of the calculation step are stored in a third data memory.

Abstract: A fluorescence lifetime imaging microscopy method with time-correlated single photon counting includes periodically exciting a sample to emit fluorescence photons, with a measurement interval being defined between each two successive excitation light pulses. A value characterizing fluorescence decay behavior is determined based on detection times of detected fluorescence photons, and imaging is performed based one the value. An analog detector signal is sampled within a plurality of sampling intervals within a respective one of the measurement intervals and is converted into a sequence of discrete signal values associated with the sampling intervals. It is determined based thereon whether more than a predefined number of fluorescence photons has been detected within the respective measurement interval.

Abstract: A fluorescence lifetime imaging microscopy method with time-correlated single photon counting includes periodically exciting a sample to emit fluorescence photons, with a measurement interval being defined between each two successive excitation light pulses. A value characterizing fluorescence decay behavior is determined based on detection times of detected fluorescence photons, and imaging is performed based one the value. An analog detector signal is sampled within a plurality of sampling intervals within a respective one of the measurement intervals and is converted into a sequence of discrete signal values associated with the sampling intervals. It is determined based thereon whether more than a predefined number of fluorescence photons has been detected within the respective measurement interval.