Methods for microscopic imaging

Abstract

When preparing or planning microscopy imaging, and / or during image processing, there is a need for more reliable, ideally fail-safe, and / or time-efficient handling of microscopy images. [Solution] A method for preparing microscope imaging, comprising acquiring a plurality of images 204 by a microscope system, annotating each of the plurality of images with metadata 201 relating to the microscope system, and grouping the plurality of images such that images that share at least partially the metadata of the plurality of images are grouped into the same image group 202.

Description

Technical Field

[0001] The present invention relates to a method for preparing microscope imaging, a method for microscope imaging, a microscope system, and the use of said system.

[0002] Background of the Invention Often, when preparing for microscope imaging, the user captures microscope images using multiple different hardware settings, compares the images with each other, and finds a hardware setting suitable for subsequent use.

[0003] However, comparing the results of multiple different settings is time-consuming and / or error-prone. This is especially true when the settings need to be managed manually. For example, restoring previous settings from existing image data to be able to capture further images in the same setting is time-consuming. After preparation, the actual microscope imaging is performed based on the appropriate hardware settings selected based on the captured images.

[0004] Therefore, there is a need for more reliable, ideally fail-safe, and / or time-efficient handling of microscope images when preparing or planning microscope imaging and / or during image processing.

[0005] Summary of the Invention The present invention relates to a method for preparing microscope imaging to solve the problem. Claim 1 defines a method for preparing microscope imaging, which includes (1) acquiring a plurality of images by a microscope system and annotating each of the plurality of images with each metadata regarding the microscope system, and (2) grouping the plurality of images such that images sharing at least partially the metadata are grouped into the same image group.

[0006] Metadata and images are correlated in that images are grouped based on metadata, for example, in a one-to-one correspondence between groups and metadata. Grouping may also mean distributing images between groups (more specifically, each image into a single group) so that images sharing the same metadata are assigned to the same group. Therefore, a group may represent specific metadata and may contain multiple images. Grouping may also mean placing images that share at least specific metadata into the same subcategory. Image groups may be represented visually or non-visually.

[0007] In this regard, images within the same group share at least partially identical, and optionally completely identical, metadata. In other words, an image group may be characterized by containing images that share at least partially, and optionally completely identical, metadata. Metadata may also serve as the basis for defining multiple different groups, each group representing specific metadata. Metadata does not need to be completely different between groups, and there may be overlaps between the metadata characterizing different groups. Overlapping metadata between groups may relate, for example, to the hardware components of a microscope, such as the light source and / or detector, or other hardware settings (see below).

[0008] Multiple groups may be provided, for example, at least three groups or at least five groups. The number of groups may vary, for example, depending on the complexity of the metadata.

[0009] Metadata may include information about microscope settings, such as the microscope's hardware settings, specific settings, or the excitation light intensity applied when capturing images. Therefore, if a group is characterized by a particular excitation light intensity, the excitation light intensity at which the image is acquired can determine its belonging to the group.

[0010] Other parameters may include the wavelength of the light source, the detection band, the lifetime setting, and distributing different detection bands across more or fewer scan passes during the acquisition of a given image.

[0011] In fluorescence microscopy, specific hardware settings may include, for example, detection bands (e.g., beam path (list of integer values), start and / or end of image acquisition, marker, and some name), laser lines (e.g., wavelength, beam path, index, intensity, relative intensity, name, abbreviation), and / or markers (dye, observed brightness, characteristic color, name, and optionally, some other user-specific information such as laboratory ID, date, and comments). Thus, for example, the marker / dye is part of the hardware settings.

[0012] If all the hardware settings parameters correspond to a specific (staining) group, the image belongs to that (staining) group.

[0013] Multiple images may be associated with the same sample, and therefore all groups may also be associated with the same sample imaged by the microscope.

[0014] The present invention provides various improved embodiments. In some embodiments, errors can be reduced compared to ungrouped images by grouping images according to metadata. In particular, metadata-based grouping can be useful for accessing images that have desired metadata, because groups "promise" to exclude images that do not have specific metadata. Furthermore, it may be possible to quickly switch between multiple different metadata, i.e., between multiple different groups, and between each image, because this can be done based on switching between groups. Comparing images from a first group to images from a second group, i.e., comparing images from different groups, may be simplified by distinguishing between the first and second groups, each defining an "umbrella" for each individual image within each group.

[0015] Alternatively or additionally, the present invention may simplify the comparison of different metadata with each other, for example, hardware settings based on corresponding captured images, and corresponding images with each other. For example, this could be useful for quickly comparing images characterized by different metadata, because images with different metadata can be assigned to different groups, which could help a user "find" images with other different metadata.

[0016] Alternatively or additionally, this may allow for improved handling of captured images. For example, handling based on identical metadata, e.g., identical hardware settings, and corresponding visibility and visual representation may be based on the provided group. The present invention may also support the creation and evaluation of microscope settings (e.g., hardware settings) for later use based on metadata.

[0017] Otherwise, without the method of the present invention, users may have to remember which settings were used when an image was acquired. Specifically, they may not be able to recognize, for example, whether two images were captured using the same settings. If they want to reuse settings, they may need to explicitly save those settings or re-import them via existing image data. Managing these settings may have to be done by the user, and therefore manually. Obviously, with a large amount of sample data, this can be prone to errors.

[0018] Optionally, the method includes adjusting the microscope system (to a microscope configuration) according to metadata of a group of images, and optionally taking / acquiring further images of the group using the metadata, in this case the microscope configuration. This may be useful for taking, i.e., acquiring further images using the same hardware settings for the group. Specifically, after preparation, actual microscope imaging is performed based on appropriate metadata, e.g., hardware settings, characteristic of a group selected based on the images taken. In particular, a group may be selected based on the images assigned to that group, for example, those that yield the best image quality.

[0019] More optionally, the metadata is loaded before the microscope system adjusts to the microscope configuration according to the metadata. This may allow the microscope to adapt to its configuration, particularly automatically. The microscope configuration may relate to the focus, light source brightness, and sensor sensitivity (scintillator, camera, semiconductor sensor, e.g., CCD).

[0020] Optionally, the microscope configuration can be adjusted by the user to a user-configured microscope configuration. In particular, the user may modify and further adjust the microscope configuration, for example, to allow it to be automatically suggested.

[0021] Optionally, the microscope configuration and / or user-adjusted microscope configuration are adjusted based on microscope feedback, which is optionally provided by optimization algorithms performed by the microscope system, and more optionally provided for the optimization of image quality, signal-to-noise ratio, and / or pixel saturation. Microscope feedback may also relate to parameters such as light intensity, focus sharpness, sample contrast, temperature variation, and / or drift in the sample stage. At least some or all of this may affect image quality and may be used to automatically adjust the settings for optimal imaging performance.

[0022] Optionally, the method further includes adding image groups to existing groups when the images cannot be grouped into existing groups. For example, when changing the hardware settings of a microscope, additional groups are added to represent groups characterized by metadata that reflects the changed hardware settings.

[0023] Optionally, the method further includes selecting a group, or optionally selecting images from a group, which is accompanied by displaying the remaining images from the group. For example, selecting a group or images from a group leads to displaying the chronological order of the captured images.

[0024] Optionally, the method further includes the display of images for a group if the selection of a group is accompanied by the display of images for that group. For example, more optionally, the selection of a group may mean that the image history of the images as they were taken is displayed for each group.

[0025] Optionally, the method may further include excluding the images of a group from the remaining groups. For example, the automatic exclusion of images not belonging to each group may be performed, for example, by not visually displaying the excluded images. This can be particularly useful for reducing errors when only images sharing common metadata, such as hardware settings, are available.

[0026] Optionally, the method further includes that taking a plurality of images includes imaging samples stained with a plurality of different fluorescent dyes. This represents a preferred embodiment and application of the method of the present invention. In other words, the method may be implemented for multi-color / multiplex microscopy and / or fluorescence microscopy. In this regard, the images may be characterized by the fluorescent dyes when the samples are stained. One group may include images of samples stained with a plurality of different fluorescent dyes. Thus, one group may be characterized by images indicating that the sample stain / dye is different but the hardware settings of the sample are the same. For example, 15 different fluorescent dyes may be used. This may be referred to as a staining group.

[0027] One or more hardware settings may belong to the staining group. The hardware settings of each staining group are the same.

[0028] Optionally, the method includes storing metadata in a memory (unit), such as a storage medium. This may enable the rapid retrieval of different metadata when desired.

[0029] Optionally, the method includes reading the metadata of the images, optionally the metadata of previously acquired or imported images, and optionally storing the metadata, for example, in a memory.

[0030] The present invention also refers to a method of microscopic imaging, including a method for preparing the microscopic imaging of the present invention, which further includes processing images for each group. This may relate to post-processing of group-based images. This can be useful for including only images sharing specific metadata for (post-)processing. Thus, since images are processed for each group, groups created during the preparation or planning of microscopic imaging may be relevant to subsequent processing.

[0031] In a further optional embodiment, the images of the group may be processed based on the metadata related to the group. For example, the hardware settings may be related to solving the problem of spectral mixing during post-processing. Thus, the hardware settings shared by the group may form the basis for processing the images of each group.

[0032] In a further optional embodiment, the group image processing may include corrections based on the metadata related to the group, such as spectral correction. For example, when processing images from fluorescence microscopy, signal crosstalk may be reduced. The correction may include using a linear matrix to unmix the image based on the hardware settings. An example thereof may be incorporating the fluorescence lifetime characteristics of the fluorescent dye. Another example is applying corrections based on fluorescence lifetime and natural background (endogenous fluorescence). This may include selecting detector signals based on photon arrival time using a time gate, or separating fluorescent components through FLIM (fluorescence lifetime imaging microscopy) decay fitting. The correction may also include noise removal and deconvolution, either in successive steps or in combination with spectral or lifetime separation. Additionally or alternatively, a trained neural network may perform the correction using spectral information and / or lifetime information from the acquired images. The metadata related to the group may include parameters for these processing steps, such as a neural network model.

[0033] Optionally, this method includes acquiring an image based on metadata and storing the image acquisition metadata as annotations in the image and / or memory. This may allow images to be acquired without checking, or even knowing, the microscope settings (i.e., microscope configuration) at the time of acquisition, because the metadata is stored in the image and / or memory, and therefore becomes available after image acquisition.

[0034] Optionally, this method includes obtaining improved metadata by retrieving metadata from memory, modifying the retrieved metadata, and creating training data based on the modified retrieved metadata. This may allow obtaining metadata optimized by training with the training data.

[0035] The present invention also refers to a microscope system having a microscope and a computer, wherein the system is configured to carry out steps of the method of the present invention. Optionally, the computer includes a processor, which is further optionally configured to carry out at least some steps of the present invention.

[0036] Optionally, the system may be configured for fluorescence microscopy. In other words, the system may be configured for multicolor / multiplex microscopy.

[0037] Optionally, a system or computer may include memory for storing metadata.

[0038] Optionally, the system further includes a display device, such as a monitor or another graphical user interface, for optional visual output, or more optionally for grouped visual output.

[0039] Optionally, the system includes a user interface for optionally initiating the display of metadata via a button included in the user interface. For example, a button may be pressed for a history function (e.g., to display all captured images) and / or to retrieve metadata.

[0040] Optionally, the user interface is configured to allow users to select options for adjusting metadata.

[0041] The present invention also relates to fluorescence microscopy, wherein the use of the system includes imaging a sample stained with a fluorescent dye in a microscope hardware setup, and grouping samples stained with multiple different fluorescent dyes and in the same hardware setup into the same group. This can be particularly useful in avoiding errors when processing images in multicolor / multiplex microscopy.

[0042] Detailed embodiments related to the present invention, as well as further advantages and features, are described below, but these examples should not be considered as limiting the invention.

[0043] As used herein, the term "and / or" includes all possible combinations of one or more of the items listed herein and may be abbreviated as " / ".

[0044] While several embodiments have been described in the context of the apparatus, it is clear that these embodiments also represent descriptions of the corresponding methods, where blocks or apparatus correspond to steps or features of steps. Similarly, embodiments described in the context of steps also represent descriptions of the corresponding blocks, items, or features of the corresponding apparatus.

[0045] At least part of the method steps, such as grouping multiple images, may be performed by a computer. At least this step may be considered a computer implementation step.

[0046] More generally, some or all of the method steps may be carried out by (or by using) hardware devices such as a processor, microprocessor, programmable computer, or electronic circuit. In some embodiments, one or more of the most important method steps may be carried out by such devices.

[0047] Depending on specific implementation requirements, embodiments of the present invention can be implemented in hardware or software. Implementation may be carried out using non-temporary storage media, such as digital storage media, such as floppy disks, DVDs, Blu-rays, CDs, ROMs, PROMs, EPROMs, EEPROMs, or flash memory, which store electronically readable control signals, and each method is implemented by (or being able to) cooperate with a programmable computer system using these control signals. Therefore, the digital storage media may be computer-readable. [Brief explanation of the drawing]

[0048] [Figure 1] This figure schematically illustrates a microscope system according to an embodiment of the present invention. [Figure 2] This figure schematically shows the underlying structure of the microscope system according to an embodiment of the present invention. [Figure 3a] This figure schematically shows the graphical user interface of a microscope system according to an embodiment of the present invention. [Figure 3b] This figure schematically shows the graphical user interface of a microscope system according to an embodiment of the present invention.

[0049] Detailed description of the invention Figure 1 schematically shows a microscope system 100 including a computer (system) 102 and a microscope 101. In this embodiment, system 100 is configured for fluorescence microscopy, but it may be a system for multicolor / multiplex microscopy.

[0050] Figure 2 schematically shows a structure 200 containing metadata, in this case microscope settings 201, and corresponding acquired grouped images 202. The metadata 201 and image groups 202 are correlated with each other in that the images are grouped based on the metadata 201. More generally, each metadata 201 correlates with a single image group 202.

[0051] Here, metadata 201 may relate to microscope settings, specifically, multiple, in this case four, different microscope (e.g., hardware) settings 203, 203a, 203b, 203c, as shown in Figure 2. Figure 2 also shows four different image groups 202, namely, a first group consisting of at least images 204, 204', 204'' characterized by common metadata 203, a second group consisting of at least images 204a, 204a', 204a'' characterized by common metadata 203a, a third group consisting of at least images 204b, 204b', 204b'' characterized by common metadata 203b, and a fourth group consisting of at least images 204c, 204c', 204c'' characterized by common metadata 203c. The number of images per group may be more or less.

[0052] Microscope settings 203, 203a, 203b, and 203c may have common parameters, such as those related to the light source and detector, but they differ in specific parameters, such as the intensity at which the image was acquired. Therefore, in this example, each of the first to fourth image groups 202 shows a different light intensity.

[0053] Therefore, if the user selects image 204 of the first group defined by hardware setting 203, the user can then view the remaining images 204', 204'' of the first group. This may help the user to quickly derive an assessment of the suitability of hardware setting 203, for example, and such assessment will take all images 204, 204', and 204'' into consideration.

[0054] Alternatively, if the user selects a first group defined by hardware setting 203, the user can receive a display of all images 204, 204', and 204'' of the first group. This may help the user to quickly derive an assessment of the suitability of hardware setting 203, for example, and such assessment would take all images 204, 204', and 204'' into consideration.

[0055] Grouping according to metadata 201 helps users handle various images. For example, when a user analyzes a second group defined by, for example, setting 203a and corresponding images 204a, 204a', 204a'', the user is assisted in evaluation by excluding all images 204, 204', and 204'' from the first group.

[0056] Structure 200 may be created by acquiring images with the microscope system 100 and annotating each of the multiple images 204,...,204a,...,204b,...,204c,... with metadata 203,203a,203b,203c related to the microscope system 100. The multiple images are then grouped such that images 204,204',204'' of the multiple images sharing the hardware configuration 203 are grouped into the same image group. This is done until all images are grouped according to metadata 201. If images cannot be grouped into existing groups, the image group may be added to an existing group.

[0057] Figures 3(a) and 3(b) schematically show metadata and images related to fluorescence microscopy, more specifically showing stained samples represented in the graphical user interface 300. Thus, Figures 3(a) and 3(b) illustrate specific applications of the present invention for spectral mixing in fluorescence microscopy with respect to fluorescent dyes A, B, C, and D. In this case, multiple images are obtained by imaging samples stained with different fluorescent dyes A to D. Therefore, samples may be stained with different fluorescent dyes and imaged in the same or different hardware settings of the microscope 101. Samples stained with different fluorescent dyes in the same hardware settings are shown in the graphical user interface 300.

[0058] For sample / specimen preparation, staining protocols, antibodies, and other parameters are defined.

[0059] A set of hardware settings is created based on a list of markers (selected by the user) and the speed selected by the user to conduct the experiment. For example, increasing the speed implies a decrease in the number of differential settings, which increases crosstalk during image acquisition. Also, staining groups are determined, representing groups of dyes used. These staining groups are generated by a computer using an algorithm to determine an appropriate (optimized) distribution for the desired settings.

[0060] Each staining group has one or more hardware configurations. Acquired images are annotated with the hardware configuration (i.e., metadata) used for image acquisition. Images are assigned to staining groups, i.e., grouped, based on their hardware configurations, and these hardware configurations are identical for images corresponding to the same hardware configuration.

[0061] In one example, metadata is loaded before the microscope system 100 is adjusted to the microscope configuration according to the metadata. The microscope configuration may relate to the focus, the brightness of the light source, the sensitivity of a sensor (scintillator, camera, semiconductor sensor, e.g., CCD), or other objects. The user may adjust the microscope configuration, for example, by changing and further adjusting the microscope configuration.

[0062] The microscope configuration and / or user-adjusted microscope configuration are adjusted based on microscope feedback, which is optionally provided by an optimization algorithm performed in the microscope system 100, and more optionally provided for the optimization of image quality, signal-to-noise ratio, and / or pixel saturation. Such feedback may relate to one or more parameters, such as light intensity, focus sharpness, sample contrast, temperature variation, and / or drift in the sample stage.

[0063] More specifically, Figures 3(a) and 3(b) schematically illustrate a graphical user interface 300 for representing grouping. All images 204,····,204''''' acquired using a specific identical hardware configuration 203 are combined into a single overall overview, which can then be filtered according to various criteria.

[0064] Specifically, in the images of Figure 3(a) and Figure 3(b), the light source and detector are identical. Other acquisition settings unrelated to the processing may differ.

[0065] The hardware configuration contains all the information needed to record a sample stained with a predetermined set of fluorescent dyes (e.g., 15 types). Each fluorescent dye is recorded by at least one detection band (channel) and excited with light of a defined wavelength. Each detection band generates one pixel image. Therefore, the "recorded image" is a group of pixel images. Since a microscope has a maximum of five detection units, it may not be possible to record all 15 fluorescent dyes in a single scan pass, and multiple scan passes may be required. Using these hardware configurations, it is possible to record a sample stained with only a subset of the fluorescent dyes, for example, one of the 15. The resulting "recorded image" still consists of 15 pixel images (channels), a small number of which (ideally one) contain the signal. In Figure 3, each row corresponds to a sample stained with only one of the dyes A, B, C, etc., but all are still recorded using the same hardware configuration that handles all 15 dyes (A, B, C, ... "15").

[0066] Metadata 201 is stored in memory (unit), for example, storage medium 104. Image metadata 201, optionally, metadata 201 of previously acquired or imported images, is read and stored in memory 104.

[0067] Images may be acquired based on metadata 201, and the metadata for image acquisition is stored as annotations in the image and / or memory 104. This may allow images to be acquired without checking, or even knowing, the microscope settings (i.e., microscope configuration) at the time of acquisition, because metadata 201 is stored in the image and / or memory, and therefore the metadata becomes available after image acquisition.

[0068] Metadata 201 may be retrieved from memory 104, and the retrieved metadata may be modified, so the system or computer includes memory for storing metadata.

[0069] System 100 or computer system 102 includes a memory 104 for storing metadata and a processor 103 for carrying out at least some steps of the method of the present invention.

[0070] System 100 includes a display device, such as a monitor or another graphical user interface 300, for the visual output of groupings, such as image group 202 and metadata 201.

[0071] The system includes a user interface 300 for optionally initiating the display of metadata 201 via a button 302 included in the user interface 300. For example, button 302 may be pressed for a history function (e.g., a function to display all acquired images) and / or to obtain metadata 201.

[0072] The user interface 300 is configured to select metadata 201, such as options for adjusting hardware settings.

[0073] System 100 enables obtaining improved metadata by creating training data based on the corrected extracted metadata. This may allow obtaining optimized metadata through training with the training data.

[0074] As shown in Figure 3(b), the image data can be switched between all available hardware settings 203, 203a, 203b, and 203c via the history list 301, thus providing a quick method for evaluating the hardware settings 203, 203a, 203b, and 203c against each other. In the example shown in Figure 3(b), setting 203 is selected, and settings 203a, 203b, and 203c are not selected. Therefore, only the group of images 204, 204', 204'',..... that correlate with setting 203 are displayed in the graphical user interface 300 at different intensities for each fluorescent dye A to D, as indicated by the register for each fluorescent dye. The four intensities belong to one, i.e., the same hardware setting. Changing one of these intensities would imply another different hardware setting.

[0075] The images are grouped in the underlying data model according to the metadata 201 at the time of capture, such as hardware settings. Therefore, the user interface 300 displays the images as they were acquired and helps simplify the handling and management of the captured images.

[0076] All images matching the currently set hardware configuration of microscope 101, for example, 203, are displayed in the overview graphical representation of interface 300. All displayed images are annotated with the same hardware configuration, which corresponds to the current hardware configuration for image acquisition. If the hardware configuration is changed in the microscope, the system checks for images annotated with the changed configuration. If so, such images with the changed hardware configuration are displayed in the user interface. Images with the previous hardware configuration are not displayed in the user interface (they are hidden).

[0077] By selecting an image, a specific image can be viewed and evaluated in the viewer. The history list 301 may provide an overview of all existing hardware settings 203, 203a, 203b, 203c and the image group 202 captured with those hardware settings 203, 203a, 203b, 203c. Entries may include information about when the image was acquired, e.g., the date, and / or information about when the first and last images in the group were taken. By selecting an entry in the history dialog / list 301, the used hardware setting 203 is set on the microscope 101, and the corresponding images 204, 204', 204'' are displayed in the overview. This allows the user to quickly switch between different settings and makes it easy to capture new images using existing hardware settings. For example, the microscope 101 is adjusted according to the metadata 201 of the images in group 202, and further images for the group are acquired using the metadata.

[0078] The unmixing strategy may determine which or how many staining groups are displayed in the graphical interface 300. For example, a staining group may be defined for each marker. Alternatively, multiple similar markers may be grouped into a single staining group. Even more alternatively, only a single staining group may be defined, and that single staining group may contain all markers.

[0079] This also makes it easier to evaluate each metadata 201 using the images of the associated group 202.

[0080] After preparing / planning and acquiring the images, the images are processed in groups. More specifically, the images of group 202 are processed based on metadata 201 associated with the group. Since the groups may reflect fluorescence imaging, the image processing includes reducing fluorescence-related issues. More specifically, the image processing of a group includes corrections based on metadata 201 associated with group 202, and optionally spectral corrections. In relation to Figures 3(a) and 3(b) and fluorescence microscopy, the corrections may include a linear matrix for unmixing the images based on image group 202, i.e., based on metadata 201, in relation to the fluorescent dye. Here, relying on group 202 is particularly useful to avoid errors in processing, such as including "wrong" images in the processing step.

[0081] Another example is correction based on the fluorescence lifetime characteristics of a fluorescent dye, more specifically, correction based on fluorescence lifetime and natural background (endogenous fluorescence). This may include selecting the detector signal based on photon arrival time using a time gate, or separating the fluorescent component through FLIM (fluorescence lifetime imaging microscopy) decay fitting. The correction may, alternatively or additionally, include denoising and deconvolution in either a series of steps or in combination with spectral separation or lifetime separation. Additionally or alternatively, a trained neural network may perform the correction using spectral and / or lifetime information from the acquired image. Metadata associated with the group may include parameters for these processing steps, e.g., the neural network model.

[0082] Some embodiments relate to a microscope 101 included in a system as described in relation to Figure 1. Alternatively, the microscope 101 may be part of a system 100 as described in relation to Figure 1, or may be connected to system 100. Figure 1 shows a schematic illustration of a system 100 configured to carry out the methods described herein. System 100 includes a microscope 101 and a computer system 102. The microscope 101 is configured to take images and is connected to the computer system 102. The computer system 102 is configured to carry out at least some of the methods described herein. The computer system 102 and the microscope 101 may be separate entities, or they may be integrated within a single common housing. The computer system 102 may be part of the central processing system of the microscope 101, and / or the computer system 102 may be part of a dependent component of the microscope 101, such as a sensor, actor, camera, or illumination unit of the microscope 101.

[0083] The computer system 102 may be a local computer device (e.g., a personal computer, laptop, tablet computer, or mobile phone) comprising one or more processors and one or more storage devices, or it may be a distributed computer system (e.g., a cloud computing system comprising one or more processors and one or more storage devices distributed to various locations such as local clients and / or one or more remote server farms and / or data centers). The computer system 102 may include any circuit or combination of circuits. In one embodiment, the computer system 102 may include one or more processors, which may be of any kind. As used herein, the processor may be intended to be any kind of computing circuit, such as a microprocessor for a microscope or microscopic component (e.g., a camera), a microcontroller, a composite instruction set computing (CISC) microprocessor, a reduced instruction set computing (RISC) microprocessor, a very long instruction word (VLIW) microprocessor, a graphics processor, a digital signal processor (DSP), a multicore processor, a field-programmable gate array (FPGA), or any other kind of processor or processing circuit. Other types of circuits that may be included in the computer system 102 may be custom circuits, application-specific integrated circuits (ASICs), etc., such as one or more circuits (communication circuits, etc.) used in wireless devices such as mobile phones, tablet computers, laptop computers, two-way radios, and similar electronic systems. The computer system 102 may also include one or more storage devices that may include one or more memory elements suitable for a particular application, such as main memory in the form of random access memory (RAM), one or more hard drives and / or one or more drives that handle removable media such as compact discs (CDs), flash memory cards, digital video discs (DVDs), etc.The computer system 102 may also include a display device, one or more speakers and a controller which may include a keyboard and / or mouse, trackball, touchscreen, voice recognition device, or any other device which enables the user of the system to input information into and receive information from the computer system 102.

[0084] A detailed description of the present invention is provided with respect to embodiments shown in the drawings. Based on the outline of the present invention, those skilled in the art will be able to conceive of obvious modifications and substitutions. These modifications and substitutions are part of the present invention to the extent that they are covered by the appended claims. [Explanation of Symbols]

[0085] 100 Microscope Systems 101 Microscope 102 Computer Systems 103 Processors 104 memory 200 Structure 201 Metadata 202 Image Group Hardware settings for 203, 203a, 203b, and 203c. 204,204',204'',204a,204a',204a'',204b,204b',204b'',204c,204c',204c'' Image 300 Graphical User Interfaces 301 History List 302 buttons

Claims

1. A method for preparing microscopic images, The microscope system (100) acquires multiple images, and each of the multiple images is annotated with metadata (201) related to the microscope system (100), and The plurality of images are grouped such that images that share at least partially the metadata (201) are grouped into the same image group (202). Methods that include...

2. The microscope system (100) is adjusted to a microscope configuration according to the metadata (201) of the group (202) images, and further images are selectively acquired for the group using the microscope configuration. The method according to claim 1, further comprising:

3. The method according to claim 2, wherein the metadata is loaded before the microscope system is adjusted to the microscope configuration according to the metadata.

4. The method according to claim 2 or 3, wherein the microscope setting configuration is adjusted by the user to a user-adjusted microscope setting configuration.

5. The method according to claim 4, wherein the microscope setting configuration is adjusted based on microscope feedback, the microscope feedback is provided by an optimization algorithm performed optionally on the microscope system, and more optionally, for the optimization of image quality, signal-to-noise ratio, and / or pixel saturation.

6. If an image group cannot be grouped into an existing group (202), add the image group to the existing group. The method according to any one of claims 1 to 5, further comprising:

7. Selecting an image from group (202) is accompanied by the display of the remaining images in the group. The method according to any one of claims 1 to 6, further comprising:

8. Selecting group (202) is accompanied by the display of the image of the said group. The method according to any one of claims 1 to 7, further comprising:

9. Remove the image from group (202) from the remaining groups. The method according to any one of claims 1 to 8, further comprising:

10. Acquiring the aforementioned multiple images allows for imaging of samples stained with multiple different fluorescent dyes. The method according to any one of claims 1 to 9, including

11. To store the metadata in memory The method according to any one of claims 1 to 10, further comprising:

12. Read metadata of an image, optionally metadata of a previously acquired or imported image, and optionally store the metadata. The method according to any one of claims 1 to 11, further comprising:

13. A method of microscopic imaging comprising the method according to any one of claims 1 to 12, Processing images by group Methods that further include the above.

14. Processing group images based on metadata associated with the group. The method according to claim 13, further comprising:

15. The processing of the group images includes corrections based on the metadata associated with the group, and optionally spectral corrections. The method according to claims 13 and 14, further comprising:

16. Acquire an image based on metadata, and save the metadata of the acquired image as an annotation in the image and / or memory. The method according to any one of claims 13 to 15, including

17. Improved metadata is obtained by retrieving the metadata from the memory, modifying the retrieved metadata, and creating training data based on the modified retrieved metadata. The method according to any one of claims 13 to 16, including

18. A microscope system (100) comprising a computer (102) and a microscope (101), wherein the system optionally includes a processor and is configured to perform the steps described in any one of claims 1 to 17.

19. The system according to claim 18, wherein the system (100) is configured for fluorescence microscopy.

20. The system according to claim 18 or 19, further comprising memory for storing metadata.

21. The system according to any one of claims 18 to 20, further comprising a display device optionally for visual output, and more optionally for grouped visual output.

22. The system according to any one of claims 18 to 21, further comprising a user interface (300) for optionally initiating the display of the metadata by a button included in the user interface.

23. The system according to claim 22, wherein the user interface (300) is configured to select options for adjusting the metadata.

24. A use of the system (100) for fluorescence microscopy according to any one of claims 18 to 23, wherein the use includes imaging a sample stained with a fluorescent dye in a microscopy hardware configuration, and grouping the samples, which are stained with multiple different fluorescent dyes and are in the same hardware configuration, into the same group.

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