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Research Based Software for Brain Tumour Segmentation, MRI Sequence Synthesis & MRI Motion Artifact Correction for Graduation Project Thesis.

CMake 0.30% Python 18.68% Dockerfile 0.45% JavaScript 1.84% TypeScript 76.22% HTML 0.08% SCSS 1.76% CSS 0.47% Shell 0.21%
cornerstone django medical-image-analysis medical-imaging microservices react segmentation typescript 3d-slicer docker orthanc

brain-tumor-segmentation-gp's Introduction

Gradutaion Project

This is a Research Based Software for Brain Tumor Segmentation & MRI Sequence Synthesis with the aid of Deep Learning and Generative AI.

Team

Team Members Sub-Team
Mahmoud Yaser Reserach & AI
Ahmed Hassan Reserach & AI
Maha Medhat Reserach & AI
Ibrahim Mohamed Software Development
Mohamed Ismail Software Development

Supervised By:

  • Prof. Meena M. Makary
    • Associate Professor, Systems & Biomedical Department Cairo University, Egypt
    • Research Scientist | Radiology, Harvard Medical School
  • Prof. Mohammed Al-masni
    • Assistant Professor, Department of Artificial Intelligence, Sejong University, South Korea.

Sponsored By:

brain-tumor-segmentation-gp's People

Contributors

1brahimmohamed avatar mohamedaismail avatar bodykudo avatar ahmedhassan187 avatar mahamedhat avatar

Stargazers

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Watchers

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brain-tumor-segmentation-gp's Issues

Feature: Interactive 3D Visualization & Reconstruction from Images

Feature description

This feature involves the development and testing of advanced algorithms to ensure a highly accurate representation of anatomical structures in three dimensions.

Use cases

  • Radiologists and healthcare professionals rely on precise 3D reconstructions to visualize and analyze anatomical structures in medical imaging.
  • Medical researchers use 3D reconstruction for detailed anatomical studies and to support clinical trials.
  • Educators and healthcare instructors can benefit from accurate 3D reconstructions for teaching and training purposes.

Benefits

  • Medical professionals, researchers, and educators can conduct detailed anatomical studies and analyses.
  • Precise 3D reconstructions empower healthcare professionals to make more informed decisions in patient care and research.

Links / Reference

Sub Task of User Story #13

Feature: Rotation and Flip Functionality

Feature description

This feature aims to implement options for image orientation adjustment. Users can rotate or flip images as needed to align them with their preferred orientation.

Use cases

  • Radiologists and healthcare professionals can adjust image orientation to match their standard viewing practices when viewing an image in the viewer.

Benefits

For whom and why?

  • The rotation and flip options provide flexibility for aligning images with the user's preference.
  • Implementing rotation and flip options contributes to a more user-friendly and adaptable application.

Links / Reference

Sub Task of User Story #7

Feature: Annotation Export

Feature description

this feature is designed to enhance the functionality of our medical viewer application. It enables users to export annotated medical images, including the annotations, in common image formats.

Use cases

  • Radiologists can export annotated images for peer review, consultations, or sharing findings with colleagues.
  • Researchers can share annotated images with research collaborators, facilitating collaboration on medical studies and projects.
  • Healthcare professionals can export annotated images for presentations or discussions within their healthcare teams.

Benefits

  • Medical professionals can easily share annotated images with colleagues, promoting efficient collaboration.
  • Enhanced sharing capabilities enable better-informed decisions and discussions in a healthcare setting.
  • Sharing annotated images simplifies communication and knowledge transfer among medical professionals.

Links / Reference

Related to User Story #10

Feature: Add measurements tracking state and connect it with the side bar

Feature description

Implement a robust state management logic for handling measurements within the application.

Use cases

  • Using Annotation Tools

    • Scenario: The user utilizes the annotation tools within the application.
    • Action: The user selects and applies different annotation tools to create and modify measurements.
    • Benefit: Provides flexibility and control for the user to make precise and varied measurements.
  • Selecting and Removing Annotations

    • Scenario: The user needs to manage specific annotations.
    • Action: The user can select any specific annotation and remove it from the workspace.
    • Benefit: Enhances user control over the annotations, allowing for easy correction and management.

Benefits

  • Improved User Experience:

    • The state management tool ensures that interactions with measurement tools are smooth and intuitive.
    • Users can easily download and import measurements, enhancing workflow efficiency and data portability.
  • Enhanced Flexibility and Control:

    • Users can manage their measurements effectively, ensuring that their workspace remains organized and clutter-free.
    • The ability to remove specific annotations allows users to correct mistakes without starting over, saving time and effort.

Feature: Medical Image Import

Feature description

This feature is about importing medical images in different formats like DICOM, & NIFTI

Use cases

  • Clinicians need to import medical images such as DICOM, NIfTI, and JPEG for patient diagnosis and care.
  • Researchers require the ability to import various image formats to conduct studies and analyze medical data.
  • Radiologists and healthcare professionals depend on the feature to efficiently access and manage patient images.

Benefits

  • Versatility in handling medical images.
  • Support for a wide range of image formats, accommodating diverse user needs.

Links / Reference

Sub Task of User Story #6

Feature: Progress Bars and Loading Screen

Feature description

this feature enhances the user experience by providing visual feedback during data processing, tasks, and loading operations. It includes the implementation of progress bars and loading screens that keep users informed about the status of ongoing activities.

Use cases

  • Users perform actions that involve data processing, such as importing large medical images or running complex algorithms.
  • Users initiate tasks that require time to complete, like data synchronization with external systems or complex image analysis.
  • The application loads data or performs calculations that may result in short delays.

Benefits

  • Offering clear and real-time feedback on the progress of tasks and data processing.
  • Reducing user frustration and anxiety by eliminating uncertainty during loading and processing times.

Links / Reference

User Story: PACS Integration

As a medical professional
I need the ability to seamlessly connect and exchange medical images with external PACS systems
So that I can efficiently access and manage patient images for diagnosis and treatment purposes.

Details and Assumptions

  • The application should support the DICOM standard for compatibility with PACS systems.
  • Secure authentication should be required to access patient images from external PACS systems.
  • Users should be able to search for, retrieve, and view patient images from connected PACS systems within the medical viewer.

Acceptance Criteria

Given I'm using the application
When I initiate a request to access patient images from an external PACS system
And the medical viewer establishes a secure connection with the PACS server using the DICOM protocol
Then the PACS system should respond by providing access to patient images stored within its repository
And I should be able to search, retrieve, and view patient images from the connected PACS system directly within the medical viewer

Feature: Window and Level Settings

Feature description

This feature is intended to implement the ability for users to adjust window-level settings. This feature empowers users to optimize image contrast for more accurate visualization.

Use cases

  • Radiologists and healthcare professionals can fine-tune window and level settings to improve the contrast of medical images when viewing an image in the viewer.

Benefits

  • Window and level settings enhance image contrast for clearer and more accurate visualization.
  • Users can customize these settings to match their specific analysis requirements and preferences.

Links / Reference

Sub Task of User Story #7

User Story: 3D Object Generation

As a medical professional
I need the ability to reconstruct and visualize 3D objects or structures from 2D medical images
So that I can enhance diagnostic capabilities and aid in treatment planning for complex medical cases.

Details and Assumptions

  • The application should allow users to select and load a series of 2D medical images for 3D reconstruction.
  • Advanced algorithms should be employed for accurate 3D reconstruction.
  • Users should have interactive control over the 3D object, including rotation, zooming, and slicing.
  • High-quality rendering should provide detailed 3D object representation.
  • Annotations and measurements should be applied to the 3D object for analysis.
  • The application should support the export of 3D object representations for sharing and storage.

Acceptance Criteria

Given I'm using the application
When I select a series of 2D medical images (e.g., MRI slices and sequences) within the medical viewer
The application processes the selected images to reconstruct a 3D object or structure
Then the generated 3D object should be displayed
And I should be able to manipulate and analyze it from various angles and perspectives
And I should be able to apply additional tools and measurements to the 3D object for diagnostic and treatment planning purposes

Feature: DICOM Studies Table

Feature description

Create a DICOM studies table for Medical Professionals to browse studies from with searching.

Use cases

Medical professionals can quickly find specific studies

Benefits

  • Increased efficiency: Saves time and effort by streamlining the process of finding relevant studies.
  • Improved accuracy: Reduces the risk of missing relevant information by allowing focused searches.
  • Enhanced flexibility: Enables users to personalize the table view based on their specific needs and search criteria.

Links / Reference

Sub Task of User Story #61

Feature: Digital Signatures

Feature description

this feature allows authorized users, such as physicians and healthcare providers, to digitally sign and authenticate reports. This ensures the validity and authenticity of medical reports.

Use cases

  • Physicians need to sign diagnostic reports to validate their findings and recommendations.
  • Healthcare providers require authentication of patient summaries and treatment plans.
  • Researchers need a mechanism for digitally signing research findings and conclusions.

Benefits

  • Validating the authenticity of medical reports, enhancing trust and reliability.
  • Ensuring that digitally signed reports cannot be tampered with or altered.
  • Meeting legal and regulatory requirements for authenticated medical documentation.

Links / Reference

Related to User Story #14

User Story: Image Viewing and Navigation

As a medical professional
I need the ability to view and navigate radiology images with clarity and ease.
So that I can analyze and explore the images effectively within the application.

Details and Assumptions

  • The image viewer should be intuitive and accessible from the main interface.
  • Users should be able to load both 2D and 3D brain images from various sources.
  • Navigation tools such as zoom, pan, and window-level settings should be available for optimal image exploration.

Acceptance Criteria

Given I'm using the application
When I select an image for viewing
And use navigation tools (e.g., zoom, pan) to explore the image
And adjust window-level settings for image clarity
Then the system should respond to my actions by updating the displayed image

User Story: Medical Image Import and Compatibility

As a medical professional
I need to be able to import brain images in various formats, including DICOM, NIfTI, and JPEG
So that I can analyze and work with these images in the system.

Details and Assumptions

  • The system should validate the format of the imported image.
  • Users should have the option to cancel or pause an ongoing import.
  • Successfully imported images should be added to the user's image library.

Acceptance Criteria

Given I'm using the application
When I select the "Import" option from the menu
And specify the file location and format
Then the system should validate the file and format
And display the imported image for viewing
And add the imported image to my image library

Feature: Reporting

Feature description

create, manage, and generate various types of reports, including diagnostic reports, patient summaries, and research findings. It offers a user-friendly interface for report creation, customization, and export in different formats.

Use cases

  • Clinicians need to efficiently create diagnostic reports for patients, including findings, recommendations, and treatment plans.
  • Healthcare professionals require a tool for summarizing patient information, medical history, and treatment progress.
  • Researchers and radiologists need to document research findings, conclusions, and statistical analysis in standardized reports.

Benefits

  • Streamlining the report creation process, saving time and effort.
  • Ensuring the consistency and accuracy of medical reports.
  • Enabling easy report customization based on medical specialties and report types.
  • Supporting the export of reports in common formats (e.g., PDF, Word) for easy sharing and archiving.
  • Enhancing the communication of medical information, improving patient care and research collaboration.

Links / Reference

Related to User Story #14

Motion Correction using stacked U-net

Feature description

Motion Artifact correction using (Movement-related artefacts (MRART)) dataset and using Stacked U-net implemented code to remove the effect of motion on the data.

Use cases

  • Used as a motion correction program
  • Used to correct the data before feeding it to any model

Benefits

-For doctors to get a better view of data free of motion artifacts.
-For the Research group to perform preprocessing of data before using it either in synthesize or in segmentation

Links / Reference

Stacked U-net

Dataset

Feature: Image Annotation

Feature description

This feature involves the development and testing of a comprehensive set of annotation tools within the application. These tools will encompass freehand drawing, text input, and shape drawing functionalities, enhancing the user's ability to mark, describe, and highlight specific elements within images.

Use cases

  • Medical professionals may employ these tools for marking areas of interest or making notes on medical images.
  • Medical researchers can make use of these tools for labeling structures, adding notes, and conducting detailed analyses of images for research and clinical studies.
  • Medical professionals may use it for active learning labeling.

Benefits

  • Medical professionals can communicate findings more clearly by annotating and marking medical images.
  • Researchers can conduct more in-depth analysis by adding detailed annotations to images.

Links / Reference

Related to User Story #10

Feature: Interactive Filtering for DICOM & NIFTI Tables

Feature description

Implement interactive filtering functionalities for both DICOM and NIFTI tables, allowing users to refine their data view based on chosen modalities and time frames.

Use cases

  • Users can quickly filter large data sets based on specific criteria.
  • Medical professionals can focus on relevant studies based on modality (e.g., X-ray, MRI) for diagnosis or analysis.
  • Researchers can explore specific time frames of NIFTI data for longitudinal studies or specific research questions.

Benefits

  • Improved data exploration: Enables efficient navigation and analysis of large datasets.
  • Enhanced user experience: Provides flexibility and control over the information displayed.
  • Increased efficiency: Saves time and effort by allowing users to focus on relevant data points.

Links / Reference

Sub Task of User Story #61

Feature: Image Retrieval

Feature description

This is for retrieving patient images from connected Picture Archiving and Communication Systems (PACS). With this feature, users can search for and retrieve images based on criteria such as patient name, study date, and accession number, all while receiving real-time updates. This functionality streamlines access to patient data and improves efficiency in healthcare settings.

Use cases

  • Clinicians and radiologists can swiftly retrieve patient images for diagnoses and treatment, ensuring timely patient care.
  • Healthcare professionals can easily access patient records during consultations and rounds, enhancing communication and decision-making.

Benefits

  • Users can swiftly search and retrieve patient images, reducing delays in diagnosis and treatment.
  • Real-time updates ensure that users have the latest patient data at their fingertips.
  • The feature enhances communication among healthcare professionals and healthcare administrators, facilitating coordinated patient care.

Links / Reference

Sub Task of #12

Feature: 3D Annotation and Measurements

Feature description

This feature is designed to empower users to apply annotations and measurements to 3D objects generated from medical images. Users can add annotations and perform measurements, such as distance measurements or volume calculations, to enhance the analysis of anatomical structures in 3D space.

Use cases

  • Radiologists and healthcare professionals can annotate and measure anatomical structures for accurate assessments and diagnoses.
  • Researchers can utilize annotations and measurements to conduct quantitative studies on medical data.
  • Educators can use this feature for teaching and demonstrating anatomical features, highlighting key points, and providing explanations.

Benefits

  • Annotations and measurements support detailed and accurate analysis of anatomical structures.
  • Researchers can quantitatively assess medical data for scientific and clinical studies.

Links / Reference

Sub Task of User Story #13

Feature: Export of Measurement Data

Feature description

This feature enhances the functionality of our medical viewer application by allowing users to export measurement data. Users can export measurement values, as well as the corresponding image regions with measurements, for documentation and further analysis. This feature streamlines the process of sharing and archiving measurement results.

Use cases

  • Medical professionals can export measurement data to include it in patient reports, ensuring that quantified findings are well-documented.
  • Researchers can export measurement data for further statistical analysis or publication in research studies and scientific papers.
  • Healthcare institutions can use this feature to create comprehensive records of patient examinations and diagnostic findings.

Benefits

  • Users can efficiently document and archive measurement data for patient records, research, or quality assurance.
  • Exported measurement data can be easily shared with colleagues, facilitating collaborative decision-making.
  • The ability to export measurement values along with their corresponding image regions ensures data integrity and clarity.

Links / Reference

Related to User Story #11

Feature: Pan and Scroll Functionality

Feature description

This feature is an essential addition to our application, ensuring smooth navigation through large images. This feature enhances users' ability to explore and navigate within images comfortably.

Use cases

  • Medical professionals can navigate through large medical images for comprehensive assessments in the viewer.

Benefits

  • Pan and scroll functionality enhances the ease of navigating through large images.
  • Implementing pan and scroll features contributes to a smoother and more user-friendly application.

Links / Reference

Sub Task of User Story #7

Feature: Statistical Analysis on Measurements

Feature description

This feature involves the development and testing of statistical calculations for measurement data, including mean, standard deviation, and range. Users can apply these statistical tools to measurement data to gain insights into data distribution and variability.

Use cases

  • Researchers can perform basic statistical analysis on measurement data collected during clinical trials or research studies to identify trends and patterns.
  • Quality control teams can use this feature to assess measurement data consistency in medical imaging processes.
  • Healthcare professionals can utilize statistical analysis to better understand patient data and trends in their practice.

Benefits

  • Users can gain insights into measurement data by applying statistical analysis and enhancing data interpretation.
  • The feature supports quality control efforts by identifying inconsistencies and variations in measurement data.
  • Statistical analysis empowers healthcare professionals and researchers to make evidence-based decisions.

Links / Reference

Related to User Story #11

Feature: Offline Access

Feature description

This feature extends the functionality of our medical viewer application by supporting access to previously retrieved images from PACS systems even when not connected to the PACS server. This capability empowers clinicians to work with patient data during remote or offline scenarios, ensuring continuous patient care and data accessibility.

Use cases

  • Clinicians can continue to work with patient images during off-site visits, such as telemedicine consultations or remote healthcare settings.
  • Medical researchers can analyze and review patient data without the need for a constant internet connection.
  • Healthcare professionals can access patient data during emergency situations when internet connectivity may be limited.

Benefits

  • Offline access ensures that clinicians can continue to provide care, even in remote or emergency situations.
  • Researchers and healthcare professionals can access patient data without being reliant on a stable internet connection.
  • The feature increases the flexibility of healthcare professionals and researchers in working with medical images.

Links / Reference

Related to User Story #12

User Story: MRI Sequences Synthesis

As a brain medical professional
I need the ability to synthesize missing MRI sequences for brain
So that I can perform comprehensive analysis and research on the synthesized images and use segmentation.

Details and Assumptions

  • The synthesis tool should be easily accessible from the main interface.
  • The application should detect the mission sequences for the study.
  • The user has the ability to choose which sequence he wants to synthesize.

Acceptance Criteria

Given I'm using the application
When I select the "Synthesis" tool
And specify the sequence I need to be synthesized.
Then the system should apply synthesis algorithms
And display the synthesized image

Feature: NIFTI Files Table

Feature description

Create a NIFTi FIles table for researchers to browse files from with searching capabilities

Use cases

Medical professionals can quickly find specific files and search for their needs

Benefits

Increased efficiency: Saves time and effort by streamlining the finding of relevant studies.
Improved accuracy: Reduces the risk of missing relevant information by allowing focused searches.
Enhanced flexibility: Enables users to personalize the table view based on their specific needs and search criteria.

Links / Reference

Sub Task of User Story #61

User Story: Motion Artifacts Correction

As a medical professional
I need the ability to automatically detect and correct motion artifacts in medical images specifically MRI for Brain
So that the ability to automatically detect and correct motion artifacts in medical images

Details and Assumptions

  • The application should provide a Motion Artifact Correction tool accessible from the main interface.
  • The system should employ algorithms to automatically detect motion artifacts in medical images.

Acceptance Criteria

Given [some context]
When [certain action is taken]
Then [the outcome of action is observed]

Feature: Progress/Loading/Status Display

Feature description

This feature is to have a progress bar, status display & loading screens to keep users informed during processes,

Use cases

  • User imports data
  • User exports data
  • Routing from one page to another

Benefits

  • Enhanced user experience by keeping users informed.
  • Increased transparency during data import processes.

Links / Reference

Feature: 3D Object Export

Feature description

This feature enables users to export & share these representations with colleagues or include them in patient records for comprehensive documentation and communication.

Use cases

  • Healthcare professionals can export 3D representations for sharing and collaboration with colleagues during patient case discussions.
  • Researchers can include 3D object representations in research papers and presentations to support their findings.
  • Medical institutions can use this feature to archive comprehensive patient records with 3D anatomical representations.

Benefits

  • Researchers can use 3D object exports for scientific publications and presentations.
  • Users can easily share 3D object representations, improving collaboration among healthcare professionals.

Links / Reference

Related to User Story #13

User Story: Internationalization (Multi-Language Support)

As a medical professional working in a multicultural environment
I need the medical viewer web app to support internationalization
So that I can easily access and understand medical imaging data in my preferred language and format.

Details and Assumptions

  • The medical viewer web app currently only supports English language and standard date/time formats.
  • Users from diverse linguistic backgrounds may find it challenging to interpret medical imaging data if it's not presented in their preferred language.
  • Standard date/time formats might not align with the conventions used in different regions, confusing users.

Acceptance Criteria

Given a medical professional from a non-English-speaking country
When they access the Medical Viewer web app
they should be able to select their preferred language from a list of supported languages

Given a medical professional viewing imaging data
When they select their preferred language
Then all interface elements, including menus, buttons, and labels, should be translated into the chosen language

Given a medical professional viewing imaging data
When they view timestamps associated with images or patient records
Then the dates and times should be displayed according to the conventions of the selected language and region

Feature: Account Lockout

Feature description

Develop an account lockout mechanism to prevent unauthorized access after a specified number of failed login attempts.

Use cases

  • After a specified number of consecutive failed login attempts, the user account is locked.
  • A locked account restricts further login attempts by the same user.

Benefits

  • Security Against Unauthorized Access: The primary benefit is enhanced security. By locking user accounts after a specified number of failed login attempts, the feature mitigates the risk of unauthorized access, data breaches, and unauthorized data exposure.

  • Protection from Brute-Force Attacks: Account lockout safeguards user accounts from brute-force attacks, a common method used by attackers to guess usernames and passwords. Locking accounts after failed attempts makes such attacks significantly more challenging.

  • Mitigation of Credential Compromise: In the event of credential compromise (e.g., due to password leaks), the feature acts as a safety net, preventing attackers from exploiting these credentials to gain access.

  • Protection of Patient Data: By preventing unauthorized access, the feature plays a crucial role in safeguarding patient data, maintaining patient privacy, and upholding data protection regulations.

Links / Reference

Linked to User Story #16

User Story: Measurements

As a medical professional
I need the ability to perform measurements on medical images
So that I can obtain accurate quantitative data for diagnostic and treatment purposes and make informed clinical decisions.

Details and Assumptions

  • The measurement tools should include distance, area, angle & perimeter measurements.
  • Real-time feedback should be provided as measurement points or contours are placed.
  • Measurement labels should be generated for easy identification, and measurement data should be exportable for documentation or further analysis.

Acceptance Criteria

Given I'm using the application
When I select the measurement tool from the toolbar
And place measurement points or contours on the image
Then the system should calculate and display the measurement value in the desired unit

User Story: Logging Service

As a software developer
I need the logging service to categorize logs based on severity levels
So that I can prioritize and address issues efficiently.

Details and Assumptions

  • The logging service currently logs all messages without distinguishing their severity levels.
  • Prioritizing and addressing issues based on their severity levels can streamline the troubleshooting process.
  • Severity levels commonly include DEBUG, INFO, WARNING, ERROR, and CRITICAL.

Acceptance Criteria

Given a software application utilizing the logging service
When an event occurs that requires logging
Then the logging service should allow the developer to specify the severity level of the log message

Given a software application generating log messages with specified severity levels
When the logging service records the messages
Then it should categorize them based on their severity level (DEBUG, INFO, WARNING, ERROR, CRITICAL)

Given a software application with categorized log messages
When developers review the logs
Then they should be able to identify and prioritize issues based on their severity levels

Given a software application with categorized log messages
When critical issues occur
Then appropriate alerts or notifications should be triggered to notify relevant stakeholders

Feature: Authentication Mechanism

Feature description

Implement the user authentication mechanism, including the login screen, credential verification, and access to the application.

Use cases

  • When a user launches the application, they are presented with a login screen.
  • The user provides their credentials (username and password).
  • The system verifies the provided credentials against the stored user database.
  • If the credentials are valid, the user gains access to the viewer's features and patient data.
  • In the case of invalid credentials, the system displays an appropriate error message and may trigger security measures.

Benefits

  • User Data Protection: The authentication mechanism ensures that sensitive patient data is protected by allowing only authorized users to access it. This enhances patient privacy and complies with data protection regulations.

  • Security Compliance: The feature helps the application comply with security standards and regulations within the healthcare industry, where data security is paramount.

  • Role-Based Access: The authentication mechanism enables role-based access control (RBAC), ensuring that users can only access features and data relevant to their roles. This prevents unauthorized access to sensitive information.

  • Privacy and Consent: The feature ensures that only authorized personnel, who have obtained patient consent, can access sensitive medical information, thus protecting patient privacy and consent rights.

Links / Reference

Related to User Story #16

Feature: Report Templates

Feature description

This Feature provides a library of customizable report templates tailored to different medical specialties and report types. Users can select and use these templates to streamline the report creation process.

Use cases

  • Clinicians and radiologists need standardized report templates for diagnostic reports.
  • Healthcare professionals require specialized templates for patient summaries, medical histories, and treatment progress.
  • Researchers and analysts need templates for research findings, statistical analysis, and research conclusions.

Benefits

  • Providing access to pre-defined templates that reduce manual report creation efforts.
  • Ensuring consistency and standardization in report formatting and content.
  • Enhancing the overall quality of medical reports and research documentation.

Links / Reference

Related to User Story #14

User Story: User Authentication and Authorization

As a user of the medical image viewer
I need the ability to authenticate myself and securely log in to the application
So that I can access sensitive patient data and features while ensuring the security and privacy of the information.

Details and Assumptions

  • The application should present a login screen where I can input my credentials (username and password).
  • Upon submission, the system should verify my credentials against the stored user database.
  • Failed login attempts should trigger appropriate error messages and security measures.
  • The application should log both successful and failed login attempts for security auditing.

Acceptance Criteria

Given I'm using the application
And I am presented with a login screen
And I provide valid credentials (username and password)
Then the system should verify my credentials against the stored user database
And I should gain access to the viewer's features and patient data
And if I provide invalid credentials, the system should display an appropriate error message
And the application should log both successful and failed login attempts for security auditing

User Story: Brain Tumor Segmentation

As a medical professional
I need the ability to perform automated and manual segmentation of brain images
So that I can isolate specific brain regions and structures for accurate diagnosis and research purposes.

Details and Assumptions

  • The segmentation tool should be accessible from the main interface.
  • Users should be able to define segmentation parameters and regions of interest (ROIs).
  • Both automated and manual segmentation methods should be supported.

Acceptance Criteria

Given I'm using the application
When I select the "Segmentation" tool
And define segmentation parameters or regions of interest
Then the system should apply segmentation algorithms
And display segmented regions on the image

User Story: Image Annotation

As a medical professional
I need the ability to annotate medical images with notes, drawings, and markers
So that can highlight specific areas of interest for diagnostic purposes and enhance the diagnostic capabilities of the application.

Details and Assumptions

  • The annotation tools should include freehand drawing, text input, and shape drawing (e.g., circles and arrows).
  • Annotations should be saved along with the associated image and should be retrievable for future reference.
  • Users should have the option to export annotated images with annotations in common image formats.

Acceptance Criteria

Given I'm using the application
When I am in the viewer preview
And activate the annotation tool
And draw a circle around an abnormality on the image
Then the system should capture the annotation and associate it with the image
And allow me to save the annotated image

Feature: Zoom Functionality

Feature description

This feature is an essential addition to our application, aimed at implementing and testing the Zoom functionality. This feature ensures that users can zoom in and out of images with adjustable zoom levels, enhancing their ability to closely examine image details.

Use cases

  • Medical Professionals can closely analyze images at varying zoom levels in the viewer.

Benefits

  • Users across different fields can benefit from zooming in and out for visualizing intricate details in large images.

Links / Reference

Sub Task of User Story #7

Feature: Measurement Tools Implementation

Feature description

This feature enables users to perform precise measurements on medical images. This feature involves the development and testing of a variety of measurement tools, including distance, area, angle, and pixel intensity measurements. Users can select from a range of measurement units and apply measurement labels to annotate their findings, enhancing the analytical capabilities of the application.

Use cases

  • Medical professionals, such as radiologists, can use measurement tools to quantify and document specific anatomical structures, lesions, or abnormalities within medical images.

  • Researchers can make precise measurements to support their studies and clinical trials, ensuring accurate and standardized data collection.

  • Educational institutions can utilize measurement tools for teaching purposes, enabling instructors and students to practice accurate image measurements for diagnostic and research scenarios.

Benefits

  • Medical professionals and researchers can make precise and standardized measurements for accurate data analysis.
  • Measurement labels and units facilitate documentation of findings, ensuring clear and reliable records.
  • The feature provides an effective educational tool for teaching and learning image analysis techniques in medical fields.

Links / Reference

Related to User Story #11

Feature: Annotation Undo/Redo Functionality

Feature description

This feature is a crucial addition to our medical viewer application. It introduces the capability to undo and redo actions during the annotation process. This functionality provides users with greater control and flexibility, allowing them to correct mistakes and refine their annotations.

Use cases

  • Medical professionals can correct annotation errors made during the image analysis, ensuring the accuracy of their findings.
  • Researchers can refine their annotations, conducting a more detailed and precise analysis of medical images.

Benefits

  • Users can easily correct annotation mistakes, promoting data accuracy.
  • Researchers and healthcare professionals can make more accurate & precise annotations by having the flexibility to undo and redo actions.
  • The feature enhances the overall usability of the application by providing greater control over the annotation process.

Links / Reference

Related to User Story #10

Feature: Report Export

Feature description

This feature allows users to export generated reports in common formats, such as PDF or Word, for printing, sharing, or archiving.

Use cases

  • Clinicians need to print and provide patients with physical copies of diagnostic reports.
  • Healthcare professionals require the ability to share patient summaries with other medical staff.
  • Researchers need to archive research findings and conclusions in a standard document format.

Benefits

  • Supporting various report export formats for different use cases.
  • Enabling the easy sharing of reports with colleagues and patients.
  • Providing the option to archive important medical and research documentation.

Links / Reference

Related to User Story #14

Feature: DICOM tag browser

Feature description

The feature is to implement a search functionality in the DICOM tag browser.

Use cases

  • Users can quickly locate DICOM tags by entering keywords or tag numbers, streamlining the process of finding specific information within DICOM files.
  • Users can navigate through extensive DICOM datasets more effectively by searching for relevant tags, reducing the time spent manually browsing through numerous tags.

Benefits

  • Improved Workflow: Radiologists, medical imaging technicians, and researchers can efficiently access the information they need, enhancing their productivity and workflow.
  • User-Friendly Interface: Adding a search functionality makes the DICOM tag browser more user-friendly, catering to both novice and experienced users.
  • Time-Saving: With the ability to search for specific tags, users can save time that would otherwise be spent manually locating tags within DICOM files.

Links / Reference

User Story: Medical Image Export

As a medical professional
I need to export medical images from the application
So that I can share them with colleagues and include them in patient records easily.

Details and Assumptions

  • The exported images should maintain high image quality and clarity.
  • Exported images should be compatible with common formats (e.g., DICOM, NIFTI, JPEG) for easy sharing and archiving.

Acceptance Criteria

Given I am viewing a medical image in the application
When I select the "Export" option
Then I should be presented with options to choose the export format, such as DICOM, NIFTI & JPEG, or other supported formats.
And I should have the ability to customize export settings, like image resolution and quality.
And I should be able to provide a file name and destination for the exported image.
And when I confirm the export, the application should generate the image in the selected format and save it to the specified location.

User Story: Reporting

As a medical professional
I need the ability to generate and manage various types of medical reports, including diagnostic reports, patient summaries, and research findings
So that I can accurately document and communicate medical information for patient care and research purposes.

Details and Assumptions

  • The application should provide a user-friendly interface for report creation and customization.
  • Users should be able to input and format text, add images, annotations, and measurements using rich text editing tools.
  • Reports should be customizable based on different medical specialties and report types.
  • Data validation should ensure that reports are complete and accurate before finalization.
  • Digital signatures should be available for authorized users to authenticate reports.
  • Reports should be exportable in common formats (e.g., PDF, Word).
  • Version control should allow clinicians to track changes and revisions over time.
  • Security measures, including role-based access control, should protect sensitive patient information within reports.

Acceptance Criteria

Given I'm using the application
When I select the reporting tool within the medical viewer
And the application provides a user-friendly interface for report creation and customization
And I input relevant medical findings, diagnoses, and other information
Then the system should generate a formatted report document based on the input data
And I should be able to review, edit, and finalize the report before saving or sharing it
And reports should be exportable in common formats (e.g., PDF, Word)

User Story: Searchable DICOM & NIFTI Data Table

As a Medical Professional & Researcher
I need searchable tables of DICOM Studies & NIFTI File
So that examine different cases & efficiently find specific data sets relevant to my research or diagnosis.

Details and Assumptions

Users can filter by:

  • Patient demographics (e.g., name, age, gender)
  • Study type (e.g., MRI, CT scan, PET scan)
  • Date Range
  • Keywords in the file description

Acceptance Criteria

Given the DICOM & NIFTI table is displayed
When the user enters a search term in the search bar
Then the table should update to show only entries matching the search term
When the user selects a filter option (e.g., study type)
Then the table should update to show only entries matching the selected filter
When the user selects multiple filter options
Then the table should update to show only entries matching all selected filters

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