Quantitative methods for optimizing the permeabilization of cellular tissues for spatial transcriptomics are provided. Also provided is an instrument for quantitatively optimizing the permeabilization of cellular tissues used for spatial transcriptomics.

The present invention enables highly accurate analysis when visualizing analysis results in spectral imaging.

An surface analysis method includes: acquiring spectral image data regarding a sample surface with use of a spectral camera; extracting n wavelengths dispersed in a specific wavelength range in the acquired spectral image data, and converting spectrums of the wavelengths in the spectral image data into n-dimensional spatial vectors for each pixel; normalizing the spatial vectors of the pixels; clustering the normalized spatial vectors into a specific number of classifications; and identifying and displaying pixels clustered into the classifications, for each of the classifications.

A method for measuring distorted illumination patterns and correcting image artifacts in structured illumination microscopy. The method includes the steps of generating an illumination pattern by interfering multiple beams, modulating a scanning speed or an intensity of a scanning laser, or projecting a mask onto an object; taking multiple exposures of the object with the illumination pattern shifting in phase; and applying Fourier transform to the multiple exposures to produce multiple raw images. Thereafter, the multiple raw images are used to form and then solve a linear equation set to obtain multiple portions of a Fourier space image of the object. A circular 2-D low pass filter and a Fourier Transform are then applied to the portions. A pattern distortion phase map is calculated and then corrected by making a coefficient matrix of the linear equation set varying in phase, which is solved in the spatial domain.

In a method for processing microscope images, at least one microscope image is provided as input image for an image processing algorithm. An output image is created from the input image by means of the image processing algorithm. The creation of the output image comprises adding low-frequency components for representing solidity of image structures of the input image to the input image, wherein the low-frequency components at least depend on high-frequency components of these image structures and wherein high-frequency components are defined by a higher spatial frequency than low-frequency components. A corresponding computer program and microscope system are likewise described.

A system for performing adaptive focusing of a microscopy device comprises a microscopy device configured to acquire microscopy images depicting cells and one or more processors executing instructions for performing a method that includes extracting pixels from the microscopy images. Each set of pixels corresponds to an independent cell. The method further includes using a trained classifier to assign one of a plurality of image quality labels to each set of pixels indicating the degree to which the independent cell is in focus. If the image quality labels corresponding to the sets of pixels indicate that the cells are out of focus, a focal length adjustment for adjusting focus of the microscopy device is determined using a trained machine learning model. Then, executable instructions are sent to the microscopy device to perform the focal length adjustment.

The present disclosure relates to a reflective FPM using a parabolic mirror, and particularly to a reflective FPM using a parabolic mirror including: a first illuminator having a first panel that is provided with numerous LED light sources and composed of a first LED array irradiating a plurality of first LED beams to a measurement object sequentially at different angles through an objective lens; a second illuminator having a second panel that is provided with numerous LED light sources and composed of a second LED array irradiating a plurality of second LED beams to the measurement object sequentially at different angles, following irradiation from the first illuminator; a parabolic mirror reflecting each of second beams generated from the second illuminator, allowing being incident on the measurement object; a lens configured to collect a beam from the measurement object to which the first and second LED beams were irradiated; and a photodetector receiving light from the lens and acquires images for each of a plurality of first and second beams.

Provided are an image acquisition device which increases a small depth of field of an objective lens to acquire a high depth of field image and an image acquisition method using the same. The image acquisition device according to an exemplary embodiment of the present disclosure is an image acquisition device which acquires an image of a subject including an image collection unit; and an objective lens unit disposed below the image collection unit, and the image collection unit generates an image in which Z-axis signals are superposed within a range corresponding to a thickness of the subject, in an area to be captured of the subject.

A microscopy includes multiple cameras working together to capture image data of a sample having a group of organisms distributed over a wide area, under the influence of an excitation instrument. A first processor is coupled to each camera to process the image data captured by the camera. Outputs from the multiple first processors are aggregated and streamed serially to a second processor for tracking the organisms. The presence of the multiple cameras capturing images from the sample, configured with 50% or more overlap, can allow 3D tracking of the organisms through photogrammetry.

A margin assessment method is provided. Under cooperation of harmonic generation microscopy (HGM) and a deep learning method, the margin assessment method can instantaneously and digitally determine whether a 3D image group generated by an HGM imaging system is a malignant tumor or the surrounding normal skin, so as to assist in determining margins of a lesion.

A method for illuminating samples in microscopic imaging methods, wherein a number m of different wavelengths λ.sub.i, with m>I and i=I, . . . , m, is selected for the illumination. For each of the wavelengths λ.sub.i a target phase function Δφ.sub.i(x, y, λ.sub.i) is predefined, wherein x and y denote spatial coordinates in a plane perpendicular to an optical axis z and each target phase function Δφ.sub.i(x, y, λ.sub.i) is effective only for the corresponding wavelength λ.sub.i. The target phase functions Δφ.sub.i are predefined depending on the structure of the sample and/or the beam shape and/or illumination light structure to be impressed on the light used for illumination. A total phase mask is then produced which realises all target phase functions Δφ.sub.i(x, y, λ.sub.i). This total phase mask is then illuminated simultaneously or successively with coherent light of wavelengths λ.sub.i such that the predefined structure of the illumination light is generated in the region of the sample.