TR2023016098A1 - Digital Pathology Image Management System - Google Patents

Abstract

The invention is a digital imaging method using an apparatus or scanner to manage digitized materials (paraffin blocks, frozen sections) used in the daily workflow of pathology laboratories in private or public healthcare institutions. The invention is designed as a system that enables the recording and listing of digitized pathological slide images via scanner devices, provides role-based access security, allows users to download images or cases, permits image anonymization, allows authorized users to assign cases to doctors, share, undo assignments, archive and unarchive, add and remove from personal collections, and facilitates laboratory workflow through functionalities that allow users to create and manage their personal collections. It also allows users to access images via a viewer module, draw annotations, take notes, and make measurements, and apply color, brightness, and contrast filters to the image. Furthermore, it allows manipulation of discrete color channels in fluorescence in situ hybridization (FISH) and immunofluorescence (IF) digital images. Thanks to its features, it enables pathologists in pathology laboratories and/or hospitals to access and examine cases. Another feature of the invention is that it minimizes the hardware dependency of hospitals by integrating with multiple digital scanner devices. This invention is designed to be web-based, allowing access from all devices with a stable internet infrastructure and a modern web browser. Users can access the invention and use all its functions via computers, laptops, phones, tablets, etc.

Description

DESCRIPTION Digital Pathology Image Management System Technical Field Related to the Invention The invention is a digital imaging method using an apparatus or scanner to manage digitized materials (paraffin blocks, frozen sections) used in the daily workflow of pathology laboratories in private or public healthcare institutions. In the current state of the technique, tissue samples obtained from patients through biopsy methods undergo laboratory processes such as tissue processing, embedding, sectioning, and staining to prepare glass slides. These slides are converted into digitized images using a scanning device. Thanks to this invention, pathologists can access digital images, enabling them to diagnose cases and determine the status of diseases by providing effective, detailed, and rapid access to case data. State of the Technique: In the current working systems of the technique, pathological examination of tissue samples taken from patients via biopsy methods begins with macroscopic examination, followed by tissue processing. At the end of this stage, the mummified tissues are placed on paraffin blocks. Sections 3-5 micrometers thick are taken from these blocks, transferred onto slides, and stained using various staining methods to make the cells visible. After staining, they are covered with a coverslip or film. The tissue sample, now on a slide, is ready for examination by the pathologist. These prepared slides are physically delivered to the pathologists. The pathologist examines the slides through a microscope and works on the diagnosis of the disease. At the end of the microscopic examination, the relevant pathologist completes their decision or additional requests regarding the case using the hospital information management system. The completed slides are received by the relevant personnel for physical archiving and are sent to the archive unit of the health institution or laboratory. For example, in a breast cancer case, the biopsy sample taken from the patient is divided into 10 separate blocks, and multiple sections are taken from each block and stained with different staining techniques. For this reason, pathologists have to evaluate many slides separately or together when examining a case. In addition, during the frozen section procedure (39), the tissue sample taken during the surgical operation while the patient is still in surgery must be physically delivered to the relevant pathologist for urgent examination. The general solution for this procedure is to have a relevant pathologist and a microscope positioned near the operating room. The disadvantages are as follows: 0 Since all materials are physically transported, delivering the relevant materials to pathologists located in different locations of the healthcare institution is quite time-consuming. 0 This transfer process causes physical fatigue on the staff, thus reducing their productivity. o There are risks of breakage or loss as a result of possible accidents during the physical transport of materials. 0 Especially during the frozen section procedure (39), the fact that the pathologist or pathologists who will examine the tissue are physically in a specific location also restricts mobility. o The confusion caused by the accumulation of cases in the pathologists' work areas over time also causes a decrease in the performance of the pathologists. Instead of physically delivering slides prepared using the traditional method to pathologists, high-quality images of all slides (27) are created in pyramid file format (28) using scanning devices (26). Digital images of tissue samples after the scanning process is completed (e.g., .svs files from Leica Aperio devices, etc.) are transmitted to pathologists digitally. The relevant pathologists can examine their cases using the digital images sent to them with the help of software or software (e.g., the imaging application of the scanning device company). However, the pathologist who needs to examine the tissue during the frozen section procedure (39) does not need to be in a specific place to complete the examination. Some digitized laboratory workflows used in the current technology, other than the traditional method, eliminate the disadvantages of the traditional method. The disadvantage that hospitals and/or laboratories that prefer this method may encounter is; In order to view the files produced by each scanner brand, it is necessary to use software developed by the manufacturer of the device. This situation reduces the flexibility of the institution by making the hospital and/or laboratory dependent on specific software. Abstract of the Invention The subject of this invention is a system developed to enable users in pathology laboratories to access, distribute, coordinate and examine digital slide images (27) with a scanner. It is a system that minimizes the physical movement of cases and increases performance and efficiency by allowing users to access case images without leaving their offices. The invention is a system that digitizes pathological slide images via scanning devices, records them in the system, lists them for users, provides role-based access security, allows users to download images or cases, permits the anonymization of images, enables laboratory workflow through functionalities such as assigning, sharing, undoing assignments, archiving and dearchiving cases to doctors, adding and removing cases to personal collections, allowing users to create and manage their personal collections, allows access to images via a viewing module, enables users to take notes by drawing annotations and make measurements, allows the use of color, brightness, and contrast filters on images, and allows manipulation of discrete color channels in fluorescence in situ hybridization (FISH) and immunofluorescence (IF) digital images. It is designed as such. Thanks to its features, it enables pathologists to access and examine cases in pathology laboratories and/or hospitals. Another feature of the invention is that it minimizes the device hardware dependency of hospitals thanks to its integration with multiple digital scanner devices. This invention is designed to be web-based so that all devices with a stable internet infrastructure and a modern web browser can access it. Users can access the invention and use all its functions through computers, laptops, phones, tablets, etc. Detailed Description of the Invention The invention works on the most digitized pathological images(27). Digital images in pyramid file format (28) created by scanner devices using access number (30) generated by PIS/APLIS (29) systems used in hospital and/or laboratory settings are called whole slide images (27). Multiple sections can be taken from tissue samples of a patient and scanned after being made into glass slides. In this way, the pre-prepared tissue sections of the patient are created as slide images with names that will contain the same accession number. At this stage, when slide images with the same accession number are captured by the system, a "Case" is created with the relevant accession number, and these slide images are associated with the relevant cases. Each case within the system is designed to contain N slide images. All cases within the invention can have 5 different states: Unassigned, Assigned, Shared, Archived, and Shared with Patient. Minimum System Requirements Hardware Network Width: 32 Mbps or higher Processor: 2 Cores 2Ghz Memory (RAM): 4 GB Software Operating System: Windows 8.1 or higher Reference List Front-end Back-end Storage PIS/APLIS services Storage units Integration services User Management Services Slide Management Services Logging Services Anonymization Services. Case Management Services. Security Services. Configuration Management Services. Image Access Services. Case Access Services. Audit/Logging Service. Data Access Layer. Image Adapters. API Endpoint Startup. Authentication Check. 1. Check failed. 2. Error code 401. API Request Check. 21.1. Request definition, parameter control and execution. 21.2. Incomplete or incorrect request. 21.3. Incomplete or incorrect parameter submission. 21.4. General error occurrence. 21.5. Error code 400. 21.6. Error code 500. Authorization Check. 22.1. Check successful. 22.2. Unauthorized access. Operation Result Check. 23.1. Code 200. 23.2. Error code 500. API Result. The conversions, 1 SON API Endpoint Bitis WSS (Whole Slide Scanner), devices that enable the creation of WSI images thanks to their lenses and high-resolution cameras, WSI (Whole Slide Image), digitized slide image. Pyramid File format: A file format created by software calculating the different distances of high-resolution images obtained from WSS devices. It has been developed to provide maximum performance in image access situations. PIS/APLIS, Pathology laboratory information system, is a software system that manages all flows within the laboratory. Access Number is information that can be used by the pathology information system to name WSI files. For example, hospitals or pathology laboratories may consist of healthcare institution users, doctors, technicians and laboratory staff. Authorized user definition is based on the discovery. Depending on the user type, doctors are in authorized mode on slides belonging to cases assigned to them and/or shared with them, while lab staff can access all cases and be in authorized mode. Reviewer users are those with access roles to WSI images, and doctors can also have this role. Users with access authorization to images are those with access roles to WSI images, and technicians, lab staff, and doctors to whom the relevant image case has been assigned and/or shared can also have this role. The system can perform hierarchical folder organization up to 2 levels. WSI images specified by user selections will be placed in folders with the names of their respective cases, converted to ZIP archive file format, and this file will be downloaded. Z-Stack: Scanner devices, during scanning, can capture a slide sample up to the maximum allowed by the hardware and scanning configuration. By reaching the zoom level, the camera module automatically focuses and takes a photograph of the relevant area. Simultaneously, by adjusting the focus level to vary within a specific range, it takes multiple photographs of the area, thus performing a scanning process. In this way, images of tissue structures (e.g., cell nuclei) on the slide with different levels of clarity at different focus levels can be transferred into the resulting WSI image after the scanning process. In short, the frozen section procedure is a pathological laboratory procedure for the rapid microscopic analysis of a sample taken during surgery. It is particularly important in determining whether there is a tumor in the tissue removed by the surgeon and whether the surgical margins are tumor-free. In the frozen section technique, the tissue taken from the patient is frozen very quickly for examination. The result obtained after the frozen section procedure is then analyzed. Upon receiving a positive result, the surgeon determines the procedure to be performed and carries out the intervention. Explanations of the Figures The attached drawings, together with the specification, show exemplary arrangements of the current specification and serve to explain the principles of the current invention together with the specification. Figure 1 is a schematic diagram of the general structure of the architectural design of the current invention; Figure 2 is a schematic diagram of the general structure of the backend layer and modules of the current invention; Figure 3 is a schematic diagram of the flow that the APIs of the backend layer of the current invention must follow; Figure 4 is a diagram showing the file format saved in the pyramid structure (28) where images of patient tissue created by the scanning devices are stored; Figure 5 is a schematic diagram showing the user roles supported by the current invention and the usage scenarios in which these roles have permissions; Abbreviation List 0 API: Application Programming Interface J SON: JavaScript Object Notation REST: Representational State Transfer WSI: Whole Slide Image WSS: Whole Slide Scanner PIS: Pathology Information System LIS: Laboratory Information System APLIS: Anatomic Pathology Laboratory Information System JW T: JavaScript Web Token DZI: Deep Zoom Image MiM: Man in the Middle AJAX: Asynchronous JavaScript And XML HTTPS: Hyper Text Protocol Secure FISH: Fluorescence In Situ Hybridization WSGI: Web Server Gateway Interface Bulus registers all cases it records as "unassigned" by default. At this stage, the case appears in the "unassigned" list and, after being assigned by authorized users to the relevant doctor(s), it appears in their "Assigned" list. From this point on, access and processing of these cases by unrelated doctors is prevented. In cases requiring a second opinion and consultation, the relevant doctors manage the cases assigned to them in the system. It can be shared with other registered doctors. Shared cases, cases whose review is complete, are sent to the archived cases list to reduce the load on other lists. Tissue samples, after being taken from the patient and undergoing pre-processing stages, are placed in the scanner device, and photographs are taken of the tissue sample at the maximum zoom distance achievable, depending on the capacity and configuration of the scanner device lens. When scanner devices zoom in with their lenses, the tissue on the slide is divided into fixed-size rectangles in the horizontal and vertical planes in successive sequences, and each scanner device lens moves through these rectangles, taking a photograph of each rectangle. The scanner device writes the photographic image data it produces through its camera into its own generated file. When the process of capturing images of all the rectangles on the tissue is complete, the scanner device The pyramid file(28) will be created by taking the lowest and highest resolution levels. A rectangle at a higher level in the pyramid file(28) is not photographed again; instead, it is completed by combining two horizontal and two vertical rectangle images taken from the lower level and reducing them by half. For example, when the images at the 3rd level are combined and reduced, the 4th level is created, and the scanner device creates all the necessary levels according to the parameters created during the scan. When the last level is created, the scanning process is finished, and the pyramid file(28) is ready to be viewed and examined. The invention has 3 different user roles: Superuser, Doctor, and Technician. Each user has different authorizations depending on their role. Doctor: These types of users are usually pathologists. By examining digitized slide images, the pathological diagnosis is determined. Technician: This type of user is usually lab technician. Their job is to perform final checks on digitized slides before they are served to pathologists. Superuser: This type of user is usually a laboratory technician or biologist. They check digitized slides, update case statuses, assign and/or share cases with doctors, archive cases, and access LIS integrations. They can also update case and slide information, perform case and slide deletion, or create manual cases. Case records registered in the system and served to pathologists retain demographic, macroscopic, localization, clinical, patient history, and initial impression information to assist pathologists. Pathologists can use this information to reach more accurate conclusions when examining relevant cases and slides. In addition, the system... The system can integrate with Pathology Information Systems (LIS) used within hospitals or laboratories and retrieve and display additional information that pathologists may need for case analysis via integration APIs. In addition to digitized slide images of recorded cases, the system allows the uploading, downloading, and viewing of other file formats as case files. These file formats include: jpeg, .png, .bmp, .mp4, .webm, .avi, .mp3, .doc, .docx, xls, xlsx, and pdf. Thanks to its viewing module, the system allows users to view image files with high performance and draw annotations on these images in various ways (freehand drawing, rectangle, ellipse, text, arrow, and triangle). The module allows users to draw sequential annotations. The viewing module allows users to navigate using a mouse or touchpad, similar to navigating a map application. It enables the use of zoom and navigation functionalities. The viewing module allows users to improve the quality of digitized slide images by adjusting color values such as brightness, contrast, and gamma, and also allows users to save their color adjustments and automatically load them later with a single click. Instead of making viewing requests on the entire slide image, the viewing module in the system uses the user's zoom level, current location, and field of view coordinates to request images only from the relevant regions, thus reducing the load on the server and shortening the request completion time, providing the user with high-performance operation. The viewing module stores successful image requests in its internal cache mechanism. When the user returns to a recently visited area, the image in the cache is used, reducing the number of network requests and This will improve performance. However, the display module has a caching mechanism on both the user and server sides. Therefore, if the image data corresponding to the coordinates the user wants to view is available, the image data stored first in the user cache and then in the server cache is used, so image requests are only processed by the system. The system allows users to create collections according to their needs, add slides to these collections, and share these collections with other users in the system. It allows downloading slide images individually, as all slides in a case, or as all cases in a collection. The invention is designed as a 3-tier architecture to improve security, scalability, and performance. The front-end, back-end, and storage layers are the three basic building blocks of this design. All layers are developed using an object-oriented approach. The invention was developed using the Python language. The software components are object-oriented. Using Oriented Programming methodologies, the systems were divided into classes and packages, reducing their interdependencies. These packages were then tested on the systems using the WSGI interface, adapting to the requirements of the operating environment. The system architecture implemented to achieve the purpose of this invention is shown in Figure 1. In addition to the invention requirements, the following architectural requirements and conditions should not be overlooked: All communication with the system must be via the HTTPS protocol. All developed APPs must perform authorization and authentication checks to complete the requested action. All developed APPs must respond in JSON data format. The server must extract header information from the request response that can provide details about the server implementation. The system must have an image cache to improve viewer performance. The system must support multiple database management systems. The system must support multiple storage areas. The system must operate with minimum network traffic by only sending requests to the areas the user wants to see on the viewer. The system must regularly check storage capacity and back up the database. The system is designed with 3 main layers: Front-end, Service, and Storage Layers. The main layers of the system are shown in Figure 1. The Front-end layer is the layer that greets users. It will be developed using the React software development framework. To ensure smoother operation of the front-end, all communication initiated by this layer will be carried out as AJAX requests over the HTTPS protocol. Since all communication will be encrypted with SSL, the system will be more resistant to possible MIM attacks. 2. The Service layer is the layer where the business logic is located. It is responsible for identity and authorization control. Case management, slide management, logging, image transfer services, and data access management are among the business operations included. Logging within the system occurs in two ways: The result of each operation will be logged to a file along with the transaction date. The input and output of each database operation will be logged to the database along with the transaction date and user. The storage layer is responsible for accessing the database and file system. It contains all the necessary modules and tools for accessing database records and slide images. Through the Slide Collector Service, it can capture newly scanned slides to the disks included in its configuration. A basic API flow has been designed to ensure the standardization of all APIs developed within the system. All APIs implemented within the system must follow the flow shown in Figure 3. 0 APIs must perform authentication at startup. 0 If the requesting user is not logged into the system, the API request will be rejected. The API should log the request and return a 401 error code. If the requesting user is logged in, but the parameters sent to the APP do not meet the APP's requirements, the API should log the request and return a 400 error code. If any error occurs during parameter checking, the API should log the status and return a 500 error code. If there are no errors in the parameter checking step, the API uses the necessary objects. If the logged-in user does not have the authority to use the APP, the API logs the status and returns a 403 error code. If the logged-in user has sufficient authority, the API fulfills the request and checks the result. If no errors are encountered during API operation, the system logs the status and returns a 200 status code. If a general error occurs during API operation, the API logs the status and returns a 500 error code. All APPs respond with J It will return the data in the SON data format. The data format returned from the server must be in the following structure: `0 code.'` This field indicates the API result. It must be present in all API results. It can only have one of the values "ok" and "error". `0 ok`: Indicates that the API request was successfully completed. `o error.' Indicates that the API request failed. `message.' (Optional): This field contains a descriptive message about the API result. It may not be present in all API results. `id` (Optional): This field shows the ID value of the object belonging to the API result. It may not be present in all API results. `data` (Optional): This field shows the API result. This field should generally be present in data fetching applications. It may not be present in all API results. The services and modules located in the backend layer are listed below. Security Service: This service provides structures that control the authorization of requests coming to the server. The JWT standard will be used for user session operations. Any unauthorized requests will be terminated and logged in this service. User Management: This service contains applications that enable the management of information belonging to users in the system. All applications in this service must pass security service control. Incident Management: This service contains APIs that provide access to and updating of information related to incidents in the system. All applications in this service must pass security service control. Slide Management: This service contains APIs that provide access to and updating of information related to slides in the system. Image Service: This service contains APIs that provide access to slide images in the system. It serves image data for requested slides to users using image adapters. It responds to image requests in DZI format. Integration Management: This service contains integration applications defined in the system. Authorized users can meet their additional information needs through these integration APIs. Anonymization Service: This service contains APPs that enable the anonymization of slides in the system. When slides are anonymized, barcodes, macro images, and other information that may belong to the patient are deleted, and the slide is renamed. Anonymized slides can then be downloaded and reviewed. Configuration Management: This service creates and keeps up-to-date the necessary configuration values for the coordinated and successful operation of other services in the system. Logging Service: This service logs all events that occur within the system in the file system. Image Adapters: These software libraries provide access to pyramid files (28) generated by different devices. Using these adapters, the system accesses the image of the requested region in the relevant pyramid files (28). Data Access Layer: This module provides the necessary tools and libraries for the system to perform database operations. An ORM library is used within the system. This allows for the unification and optimization of database operations performed by other software components. It also eliminates background database dependency. Audit/Logging: This module ensures that all changes made to the database are logged in a separate table. This allows for the logging of all database changes later. The system also includes a viewer module for reviewing slide images. Using the width and length information of the slide image, the viewing module calculates the zoom range and minimum and maximum positions the user can move within during operation. The viewer module calculates the distance required to fit the desired slide image onto the user's screen, and directs the user's viewport to the correct level and location. After this step, it calculates rectangular areas (tiles) of equal width and height in a grid structure on the user's screen and makes an AJAX request to the server for each tile. The address format used by the server for each tile request is DZI. This address format, which conforms to RESTful API logic, sends the slide identifier, level, and coordinate information of the location to the server. The back-end structures of the invention use this information sent to them by the front-end structures to access the slide image the user wishes to view. They read the image segment with the correct coordinates from the slide file at the requested zoom level, convert it to JPEG image format, and transfer it to the front-end. The front-end structures complete the request by drawing the image segments transferred from the back-end structures onto the correct regions on the user's display devices (computer screen, phone screen, etc.) that they have previously calculated. This process chain is repeated for all the calculated rectangular areas on the user's screen, allowing the user to move around the slide image along the X, Y, and Z axes and examine the slide image. Furthermore, the image data from the back-end structures is cached in the front-end structures. When user movement along the X, Y, or Z axis is detected, a cache check is performed before requesting an image to the backend. If the image with the relevant zoom and coordinate information is found in the cache, the request is not made to the backend; instead, it is read from the cache, reducing the load on the backend and improving performance. The viewing module included in Bulus allows users to make drawings and take notes on the slide image in various ways. Bulus supports freehand drawing, rectangle, ellipse, polygon, arrow, triangle, and text drawings. While each drawing type has a different drawing method, Bulus includes separate clickable elements on the viewing module for each drawing type. After zooming in and out on the desired area of the slideshow, the user activates the desired drawing type by clicking on the relevant element in the viewer module. They can then complete the drawing process using pointer devices (such as a mouse) via drag-and-drop or clicking. Users can select their drawings by double-clicking on them and change the fill and line colors. The drawings created by users have the necessary elements within the module for later hiding/showing and deleting. The drawing methods for the drawing types included in the invention are explained below within the viewer module. • Freehand drawing: In this drawing mode, after activating the mode, the user can click on a point on the drawing module and continue drawing by holding down the pointer devices (e.g., mouse) and moving the mouse along the specified areas. The drawing module will close at the point where the pointer devices are released, and the drawing will be complete. The drawing created by the user will be a line containing the points where the pointer devices were moved. • Rectangle drawing: In this drawing mode, after activating the mode, the user can click on a point on the drawing module and continue drawing by holding down the pointer devices (e.g., mouse) and moving the pointer devices along the specified areas. The drawing module will close at the point where the pointer devices are released, and the drawing will be complete. The point where the user first started drawing and the point where they released the pointer devices will be the top left and bottom right corners of the desired rectangle, respectively, and a rectangle will be drawn on the user's screen. o Ellipse drawing: In this drawing mode, after activating the mode, the user can click on a point on the drawing module and continue drawing by holding down the marker devices and moving them along the desired areas. When the marker devices are released, the drawing module will be deactivated and the drawing will be complete. An ellipse drawing with height, radius, and width radii will be drawn on the user's screen, fitting within a quadrilateral area using the point where the user first started drawing and the point where they released the marker devices as corner points. o Polygon drawing: In this drawing mode, after activating the mode, the user can draw by clicking on the desired points on the drawing module. The system creates a polygon by drawing a line segment between each point clicked by the user and the previous clicked point. After clicking all the desired points, the user can complete the drawing by clicking on the first point they clicked. Arrow Drawing: In this drawing mode, after activating the mode, the user clicks on a point on the drawing module and continues drawing by holding down the marker devices and moving them across the areas. The drawing module will close and the drawing will be completed at the point where the marker devices are released. A line segment with an arrowhead will be drawn on the screen between the point where the user started drawing and the point where they released the marker devices, completing the drawing process. Triangle Drawing: In this drawing mode, after activating the mode, the user can click on a point on the drawing module and continue drawing by holding down the marker devices and moving them along the marked areas. When the marker devices are released, the drawing module will close and the drawing will be completed. A triangle will be drawn on the screen in the direction and orientation between the point where the user started drawing and the point where they released the marker devices, completing the drawing process. Text Drawing: In this drawing mode, after activating the mode, the user will be asked to provide a drawing note to be placed on the screen after clicking on a point on the drawing module. The text provided by the user will be written at the point clicked by the user on the screen, completing the drawing process. The viewer module within the invention has elements that allow users to rotate images around the center of the image. Users can rotate images to any desired degree, and during this process, any drawings on the viewer module are also rotated along with the images. The viewer module included in the invention allows users to adjust the brightness, contrast, gamma, black balance, and white balance, and if available, the z-stack(3 8) level values of the slide images they are reviewing, save their adjustments, and assign and delete the saved adjustments as defaults. A slide image can have more than one z-stack(3 8) level depending on the hardware, features, and configuration of the scanner device during scanning. The viewer module allows the adjustment of the z-stack(3 8) level value of the slide image, enabling the user to achieve different levels of focus for the area they wish to view. The viewer module allows modification of color channels specific to the slide, depending on the type of slide to be examined. Slide types and the color channels and color space values they support are explained below. 1. Brightfield slides: 0 Brightness: Allows the user to change the brightness values of the slide images provided. 0 Contrast: Allows the user to change the contrast value of the slide images provided. 0 Grayscale: Allows the user to view the slide in grayscale by increasing or decreasing the grayscale of the slide images provided. 0 Hue: Allows the user to change the colors of the slide images provided to other colors in the color scale. Colors in the visible color spectrum are normalized to a range of 0-255, allowing the user to modify the color value in the images served to them by selecting a value within this range. 0. Saturation: Allows the user to increase or decrease the saturation of the colors in the slide images served to them. 2. FISH/IF slides: Unlike bright field slides, FISH and IF slide files can have different color channels (red, green, and blue) depending on the hardware and features of the scanner device. Scanner devices save information about the color filters they use during scanning into the slide files. Bulus reads and provides color channel information in these types of files, allowing users to adjust the black, white, and gamma values of the color channels in the images contained within the slide. By displaying the histogram values of the channels within the slide separately, Bulus allows users to make the necessary adjustments more effectively. Some examples of color channels that can be found in FISH and IF slide files are listed below: o Spectrum Orange o Spectrum Green o Spectrum Aqua Usage Scenarios The usage scenarios of the system's main features, along with user types, are shown in Figure 3. This usage scenario is the same for every user type. 1.1 Access to Unassigned, My Cases, Shared with Me, and Archived Cases: These usage scenarios allow doctors to access cases. Doctors can access unassigned, archived, assigned, and shared cases. 1.2 Access slides, use annotation features: These use cases allow doctors to access and review slide images in cases, and draw annotations in various ways. 1.3 Upload standard files to cases: These use cases define how doctors can upload, download, and remove standard files from cases. Standard files can be images, audio, video, PDFs, etc. 1.4 Create, delete, share collections: These use cases define how doctors can create, delete, edit collections, assign cases to these collections, and share these collections. 1.5 Download cases, slides, collections: These use cases define how doctors can download slide files. The slides to be downloaded can be specific slides from a case, all slides from a case, or all slides from all cases in a collection. Superuser: 2.1 Access slides, use annotation features: These usage scenarios allow superusers to access and review slide images in cases, and draw annotations in different ways. 2.2 Upload standard files to cases: These usage scenarios define how superusers can upload, download, and delete standard files to cases. Standard files can be images, audio, video, PDFs, etc. 2.3 Create, delete, share collections: These usage scenarios define how superusers can create, delete, edit collections, assign cases to these collections, and share these collections. 2.4 Download cases, slides, collections: These usage scenarios define how superusers can download slide files. The slides to be downloaded can be specific slides from a case, all slides from a case, or all slides from all cases in a collection. 2.5 Using Integration Apps: These use cases describe how superusers can use integration apps if an integration API is defined in the system. 2.6 Anonymize cases and slides: These use cases describe how superusers can anonymize slides for sharing outside the organization. Anonymized slides are those that have been cleaned and do not contain any patient information. Anonymized slides can be downloaded later. 2.7 Share cases and slides outside the organization: These use cases describe how superusers can share desired cases or slides with users outside the organization for a specific period of time. 2.8 Assign, Share, Archive, Edit, Delete: These use cases describe how superusers can assign cases to doctors, share cases with doctors, edit and delete cases, and archive cases. 2.9 Access Assigned, Unassigned, and Archived Cases: These use cases allow superusers to access cases. Superusers can access unassigned, archived, and cases assigned to any doctor. Technician: 3.1 Access Assigned, Unassigned, and Archived Cases: These use cases allow technicians to access cases. Technicians can access unassigned, archived, and cases assigned to any doctor.

Claims (1)

1.