# US 12,181,413 B2 · Method, computer program, and apparatus for adapting an estimator for use in a microscope > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 12,181,413 B2 - Document ID: US12181413B2 - Status: Granted - Kind: B2 - Application number: 18/607,821 - Filed: 2024-03-18 - Published: 2024-07-04 - Granted: 2024-12-31 - Earliest claimed: 2020-08-07 - Assignees: Abberior Instruments GmbH - Applicants: Abberior Instruments GmbH - Inventors: Roman Schmidt - Web page: https://patentgrep.com/patent/US12181413B2 ## CPC - G01N 21/6458: {Fluorescence microscopy (fluorescence microscopes per se G02B21/0076 and G02B21/16)} - G02B 21/0076: {arrangements using fluorescence or luminescence} - G02B 21/0072: {details concerning resolution or correction, including general design of CSOM objectives} - G02B 21/008: {Details of detection or image processing, including general computer control} - G02B 21/16: adapted for ultraviolet illumination {; Fluorescence microscopes (G02B21/0076 takes precedence)} - G06T 7/0014: {using an image reference approach} - G06T 2207/10064: Fluorescence image - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - G02B: OPTICAL ELEMENTS, SYSTEMS OR APPARATUS - G06T: IMAGE DATA PROCESSING OR GENERATION, IN GENERAL ## Abstract The present invention is related to a method, a computer program, and apparatus for adapting an estimator for use in a microscope for estimating a position of an emitter in a sample based on a method, in which the sample is illuminated with light at one or more sets of probe positions and fluorescence photons are acquired for the sets of probe positions. The invention is further related to a microscope, which makes use of such a method or apparatus. The sample is illuminated with light at one or more sets of probe positions and fluorescence photons are acquired for the sets of probe positions. Photon counts of the acquired photons are then added to vectors of photon counts or sums of photon counts are determined for the sets of probe positions. A value representative of background noise is determined and used for adapting the estimator in real-time. ## Claims ### Claim 1 A method for estimating positions of individual emitters in a sample, comprising: scanning a sample region on a set of relative probe positions around an estimated position of an emitter with an excitation donut, and detecting fluorescence at the respective probe positions, wherein during scanning the emitter is in a dark state; determining background fluorescence from the detected fluorescence; scanning another emitter on a set of relative probe positions around the estimated position of this other emitter with an excitation donut, and detecting fluorescence at the relative probe positions; and estimating, by an estimator, a position of this other emitter from the detected fluorescence and the relative probe positions, taking into account the previously determined background fluorescence. ### Claim 2 (depends on 1) The method of claim 1, wherein the positions of the emitters are estimated in an iterative process. ### Claim 3 (depends on 2) The method of claim 2, wherein in each iteration, fluorescence at the respective relative probe positions is detected until a photon limit, corrected by the determined background fluorescence, is reached. ### Claim 4 (depends on 2) The method of claim 2, wherein an updated background fluorescence is determined from fluorescence detected for a set of relative probe positions around an emitter that has changed to a dark state. ### Claim 5 (depends on 2) The method of claim 2, wherein the estimator uses a calibration polynomial, which is specific for each of a plurality of iterations. ### Claim 6 (depends on 2) The method of claim 2, wherein the determined background is specific for each of a plurality of iterations. ### Claim 7 (depends on 1) The method of claim 1, wherein the estimator is adapted in such way that an expectancy value of the determined background fluorescence is subtracted from photon counts before estimating a position of an emitter. ### Claim 8 (depends on 1) The method of claim 1, wherein the sets of relative probe positions are illuminated multiple times. ### Claim 9 (depends on 1) The method of claim 1, wherein the sets of relative probe positions each comprise three or more probe positions, which are arranged rotationally symmetric on a circle. ### Claim 10 (depends on 9) The method of claim 9, wherein opposing probe positions of a set of relative probe positions are illuminated in sequential pairs. ### Claim 11 (depends on 1) The method of claim 1, wherein the estimator is a least-mean-squared estimator. ### Claim 12 (depends on 1) The method of claim 1, wherein the estimator uses a pattern for estimation, which has a probe position in the center, and wherein a ratio of signal and background is determined using the determined background fluorescence. ### Claim 13 (depends on 1) The method of claim 1, further comprising performing a pre-localization procedure, in which a region of interest is scanned in search for fluorescing emitters, wherein different locations of the region of interest are illuminated with an excitation beam, fluorescence is detected, and background fluorescence is determined from the detected fluorescence. ### Claim 14 (depends on 13) The method of claim 13, wherein in the pre-localization procedure, a pinhole is sequentially projected to probe positions. ### Claim 15 (depends on 13) The method of claim 13, wherein in the pre-localization procedure, imaging conditions are chosen such that most non-background emitters are in their dark state. ### Claim 16 (depends on 1) The method of claim 1, wherein for determining whether fluorescence from an emitter is detected, the sum of photon counts for a set of relative probe positions is compared with a threshold derived from an applicable current estimated background. ### Claim 17 (depends on 16) The method of claim 16, wherein the sums of photon counts are added to a histogram. ### Claim 18 (depends on 17) The method of claim 17, wherein the background fluorescence is derived from a peak of the histogram. ### Claim 19 (depends on 1) A non-transitory computer readable storage medium comprising instructions, which, when executed by a computer, cause the computer to perform a method according to claim 1 for estimating positions of individual emitters in a sample. ### Claim 20 A MINFLUX microscope comprising a controller, wherein the controller is configured to estimate positions of individual emitters in a sample by: scanning a sample region on a set of relative probe positions around an estimated position of an emitter with an excitation donut, and detecting fluorescence at the respective probe positions, wherein during scanning the emitter is in a dark state; determining background fluorescence from the detected fluorescence; scanning another emitter on a set of relative probe positions around the estimated position of this other emitter with an excitation donut, and detecting fluorescence at the relative probe positions; and estimating, by an estimator, a position of this other emitter from the detected fluorescence and the relative probe positions, taking into account the previously determined background fluorescence.