Advancing Colorectal Cancer Detection: Seamless AI Integration in the Pathologist’s Workflow
As pathologists, we understand that the detection of colorectal cancer is a task that demands precision, experience, and efficiency. Every day, we navigate the complexities of interpreting stained slides, identifying subtle abnormalities, and ensuring that each diagnosis is as accurate as possible. However, even with the best practices, the potential for human error and the time-intensive nature of our work can be challenging. The integration of advanced AI tools into our workflow offers a way to enhance our diagnostic accuracy, streamline processes, and ultimately improve patient outcomes.
Integrating AI with Traditional Staining Techniques
Stainings such as H&E and IHC are the backbone of our diagnostic toolkit, providing essential insights into cellular and tissue structures. While these techniques are indispensable, interpreting complex or borderline cases requires a significant investment of time and expertise. AI tools, like the HyperCRC-NET model from HS Analysis GmbH, are designed to seamlessly integrate with these traditional methods, offering a complementary layer of analysis that enhances our ability to detect malignant changes, even in their earliest stages.
By incorporating HyperCRC-NET into your workflow, you can efficiently flag areas of concern that might be subtle or easily overlooked. This tool operates in the background, analyzing stained slides with precision and alerting you to potential malignancies that warrant closer examination. This not only reduces the likelihood of missed diagnoses but also frees up time for more nuanced analysis, allowing you to focus on cases that require your expert attention.
Streamlining Workflow with AI-Enhanced Data Management
Once potential malignancies have been identified, the task of compiling and reporting data begins. The HSA KIT software is designed to integrate seamlessly into your existing workflow, automating the tedious aspects of data management. Instead of manually compiling data and generating reports, the HSA KIT allows you to export all relevant diagnostic information into organized Excel sheets with minimal effort.
This automation ensures that your reports are comprehensive, consistent, and ready for multidisciplinary team meetings or patient consultations. The software’s intuitive interface is tailored to the needs of pathologists, providing quick access to critical information and facilitating easy navigation through stained images. With features like a navigation preview window and a versatile tool panel for annotations, HSA KIT ensures that your focus remains on diagnostic precision, rather than on navigating complex software.
Customizable AI for Tailored Diagnostic Precision
A significant advantage of the HSA KIT software is its flexibility in AI integration. You can import custom models and even train new ones on-the-go, allowing the AI to adapt to the specific needs of your practice. This means the AI can be fine-tuned to recognize the unique staining patterns or biomarkers that are most relevant to the colorectal cancer cases you encounter, ensuring that the tools you use are tailored to your specific diagnostic requirements.
This customization capability is invaluable for practices dealing with diverse patient populations or unusual case presentations. By adjusting the AI models to reflect these nuances, you can enhance the precision of your diagnoses and ensure that your workflow is optimized for the challenges you face daily.
Enhancing Your Workflow with AI
The integration of AI tools like HyperCRC-NET and HSA KIT into your pathology workflow doesn’t just promise improvements in accuracy and efficiency—it delivers a more streamlined, consistent, and reliable diagnostic process. These tools are designed to complement and enhance your existing practices, allowing you to leverage AI’s strengths while maintaining full control over the diagnostic process.
Incorporating AI into your workflow allows you to focus on the most critical aspects of your work, confident that routine tasks are being handled with precision and consistency. The result is a workflow that is not only more efficient but also more capable of delivering the high-quality, reliable diagnoses that your patients depend on.
The future of pathology is not just about keeping pace with technological advancements—it’s about integrating these advancements in ways that make our work more effective and our outcomes more certain. With tools like HyperCRC-NET and HSA KIT, that future is here, offering pathologists like you the means to elevate your practice and continue delivering exceptional care.
HSA KIT
Advanced Capabilities of HyperCRC-Net
The HyperCRC-Net module within HSA KIT is highly effective in categorizing different types of glands within the Base ROI (Region of Interest):
- Healthy glands: Indicated in green
- Adenoma glands: Indicated in yellow
- Carcinoma glands: Indicated in red
- Other tissues: Such as muscle, adipose, or stroma, indicated in blue
Precision Annotation and AI Training
The HSA KIT software includes professional-grade annotation tools, enabling users to zoom in to the pixel level for precise labeling. Clients can train existing deep learning (DL) models or optimize them for specific applications. Additional annotations can be added to existing structures to improve detection accuracy. The data recorded during training, known as Ground Truth Data (GTD), forms the basis for high-quality DL models.
Ground Truth Data (GTD) creation
Mean Average Precision (mAP) and Performance Metrics
Mean Average Precision (mAP) is a key metric used to evaluate object detection models. It calculates the average precision across different object detection thresholds, providing a comprehensive measure of the model’s performance. The core metrics that contribute to mAP accuracy are the Confusion Matrix, Intersection over Union (IoU), Recall, and Precision. The mAP is determined by finding the Average Precision (AP) for each class and averaging it across multiple classes.
Confusion Matrix and Evaluation Metrics
The Confusion Matrix is a tool that allows users to assess a model’s performance by comparing its predictions with actual outcomes. It helps identify the types of errors made by the model and calculates various evaluation metrics such as accuracy, precision, recall, and F1 score.
Training Data and Model Refinement
The samples used to train the DL model were obtained from diseased patients, with tissues stained using HE staining. Digitalized slides were loaded into the HSA KIT software, and the target area (Base ROI) was annotated and classified into healthy, adenoma, or carcinoma categories. The model was initially trained with 1,647 GTD, but after identifying shortcomings, more GTD were created, and the model was retrained with 4,631 GTD. The distribution of classes and their percentages in the created data are detailed in the table below:
HyperCRC-Net Module Variants
The HyperCRC-Net module offers two versions:
- Type 1: Based on the Vision Transformer (ViT) architecture, focusing on instance segmentation.
- Type 2: Utilizing the U-Net architecture, focusing on segmentation.
After the model has been trained and the project has been completed, the HSA KIT software provides the information required to understand the results in a sheet format, including the name of the files, the number of objects (structures), the dimension of the analyzed areas in square meters within specific Base ROI (Region of Interest) area.
Interpretation of Results
Using the HSA KIT, metrics can be used to compare the performance of different models and identify patterns or trends that offer insights into model accuracy. By analyzing graphs and data, informed decisions can be made regarding a model’s suitability for predicting colorectal cancer.
Increasing the amount of Ground Truth Data (GTD) used to train models significantly enhances their prediction accuracy.
For HyperCRC-Net Type 1 using Instance Segmentation, we observe a clear trend: as the number of GTDs increases, the loss function decreases, while the Mean Average Precision (mAP) improves. This demonstrates that the model is effectively learning to identify and segment instances within the dataset.
Similarly, for HyperCRC-Net Type 2, which focuses on segmentation, an increase in GTDs leads to a reduction in the loss function and an improvement in the Intersection over Union (IoU) metric. This indicates that the model is becoming more accurate in aligning its predictions with the actual data.
HE and Ki67 staining
HE and Ki67 Staining in Histopathology
Hematoxylin and Eosin (H&E) staining is a fundamental technique in histopathology, providing essential information for diagnosing a wide range of diseases. Hematoxylin stains cell nuclei blue or purple, while Eosin stains the cytoplasm and extracellular elements pink or red, enabling clear visualization of cellular structures.
Ki-67 staining, an immunohistochemical technique, detects and maps the expression of the Ki-67 protein in cells. Ki-67 is associated with cell proliferation and is used in cancer research to evaluate tumor growth, assess the proliferative index of tumors, and predict prognosis or treatment response.
HSA KIT: A Comprehensive Tool for Histopathological Analysis
The HSA KIT software provides a one-stop solution for detecting colorectal cancer using various stains. Large datasets of annotated histopathology images are used to train the HyperCRC-Net module, enabling accurate detection, segmentation, classification, and grading of colorectal cancer.
HSA Manipulation Tool
The Manipulation Tool in HSA KIT combines advanced AI technology with microscopy expertise to enable precise and efficient image analysis. Key features include:
- Handling Large Data Sets: Works with Whole Slide Images (WSIs) of any size, offering flexibility in image analysis.
- User-Friendly Labeling Tools: Provides intuitive usability with customizable editing options.
- Information Transfer: Allows polygons and annotations to be transferred between files in split-screen view.
By transfering annotations one can identify and compare the same cells and structures in different stainings. This can help increase the accuracy of diagnosis and facilitate research. Transfering annotations from one stain to another can also aid in the interpretation of histological sections. For example, one can use one staining to mark specific elements and then transfer that annotation to another staining to mark other structures.
Rotating images 90 degrees can help reveal details that may not have been visible due to the orientation of the image, thereby gaining a better understanding of the object’s structure and composition. Flipping images can also help you see certain features better by flipping the image horizontally or vertically.
HSA Case Viewer
Comprehensive Patient Information
Each case in the HSA Case Viewer includes a summary of the patient, clinical evaluation, diagnosis, and comments, alongside the tissue sections and other in-depth information. This holistic view of the patient’s condition supports well-informed clinical decisions and the development of personalized treatment strategies.
Continuous Learning and Improvement
The ability to access and review previous cases stored in the platform’s database supports continuous learning and improvement in medical practices. Additionally, the integration between the case viewer and file viewer ensures that all pertinent information is easily accessible, allowing for a thorough examination of tissue sections directly from the case viewer.
Advanced Heatmap tool
Visualizing Colorectal Carcinoma with Heatmaps
The heatmaps generated by HSA KIT vividly display colorectal carcinoma areas. Warm colors, such as yellow and red, represent regions with higher intensity detected by the model, while blue regions indicate lower priority pixels for the respective class.
The Importance of Training Data and Explainability
Understanding an AI system requires careful attention to the underlying training data and procedures. To improve a model’s explainability, it’s essential to map the trained model back to the dataset used for training and analyze that data closely. Teams need to determine where the training data originates, whether it contains any biases, and how to mitigate those biases during the model’s design process.
The xAI tool in HSA KIT is designed to find and highlight target areas containing specific signals, providing visual explanations without requiring architectural changes or additional training. By activating the “Heatmap” icon and selecting a structure, users can view the results in a clear and visual format.
Heatmap Tool for Enhanced Visualization
The HSA KIT includes a powerful heatmap tool that provides slide-level scores for specific endpoints. These heatmaps visually display the likelihood of each endpoint being present at every pixel on the slide, making it easier for professionals to diagnose and treat cancer patients. As technology continues to evolve, this approach will make cancer detection and treatment increasingly precise and effective.
Understanding Deep Learning Model Decisions with Heatmaps
The advanced heatmap tool in HSA KIT is particularly useful for interpreting the decisions of trained Deep Learning (DL) models. Once a DL model has been trained on colorectal biopsy files, the heatmap tool allows users to visualize carcinoma areas clearly. By activating the xAI and heatmap features, you can see the most important pixels the model uses to classify carcinoma. Red regions highlight the pixels that are crucial for the model, while blue regions indicate pixels used but not prioritized. This visualization helps users understand the model’s decision-making process both during and after training.
Custom Modules in HSA KIT
HSA KIT: The Ultimate Tool for Custom Deep Learning Models
In a lab setting, the HSA KIT is your go-to solution for developing and training custom deep learning models. With hundreds of scalable modules available, this kit is built to meet long-term requirements and create flexible solutions that adapt to your evolving needs. Whether you’re tackling a complex project or a simpler task, HSA KIT has everything you need to get started.
Tailored Solutions for Maximum Value
Out of the hundreds of custom modules available, only a selection is shown in the image above. Our client-centric approach ensures that we design and deliver modules that align perfectly with your specific goals and objectives, guaranteeing maximum value and satisfaction.
Comprehensive Tools for Every Stage of Your Project
The HSA KIT includes all the essential tools for successful deep learning projects, from data preprocessing to model building and evaluation. Its user-friendly interface and comprehensive documentation make it accessible even to beginners, allowing anyone to quickly learn and leverage this powerful tool.
If you’re seeking an all-in-one solution for your deep learning needs, the HSA KIT is the perfect choice.
Digitalisation of slides
Digitalization of Slides with HSA KIT
The HSA KIT is a highly versatile tool designed to work seamlessly with top-tier automatic slide scanners like the Leica GT 450. It integrates effortlessly with these devices, enabling quick and precise slide scanning. With cutting-edge features such as automated slide handling and adjustable scanning parameters, HSA KIT enhances your digital pathology infrastructure, allowing users to personalize and streamline the scanning process to suit their specific needs. Whether you’re in pathology or research, HSA KIT is an excellent choice for seamless integration with your existing technology.
Affordable Manual Scanning with HSA Scan
In addition to supporting high-end automatic scanners, HS Analysis offers an affordable alternative with the HSA Scan software. This solution allows you to manually digitize slides directly on your current microscope, creating Whole Slide Images (WSI). This approach provides greater flexibility and control over the scanning process, making HSA KIT a versatile option for labs with various microscope models. The software is user-friendly and easy to navigate, ensuring efficient scanning and image processing.
Cost-Effective Slide Digitization
By enabling the creation of manual WSIs, labs can save on the cost of expensive scanners while still producing high-quality digital images. The combination of HSA KIT and HSA Scan software offers a cost-effective solution for labs looking to digitize their slides without compromising on quality or control. Manual scanning converts slides into digital files that can be easily managed, trained, and analyzed using AI models in HSA KIT. This allows labs to efficiently handle their slide inventory and access digital versions of their slides from anywhere.
User-Friendly and Advanced Image Analysis
The software’s intuitive interface allows for easy navigation and customization of scanning settings to meet your lab’s specific needs. Integration with HSA KIT enables advanced image analysis and interpretation, providing valuable insights for both research and diagnosis. Overall, HSA Scan offers a comprehensive solution for labs aiming to streamline their slide digitization process while maintaining strict quality control.
Upgrade Your Microscope with HSA SCAN A
Transform your existing microscope into an automated microscope station with HSA SCAN A for a low-cost, high-quality scanning solution. This upgrade delivers consistent results in a short period of time without the need for manual adjustments.
How It Works: HSA SCAN A requires only the dimensions of your microscope and any specific requirements you may have. We’ll deliver a custom-fit stand and motor tailored to your microscope, ensuring seamless integration and ease of use.
Benefits of HSA SCAN A:
- Accurate and Quick Scanning: Automates the scanning process for precise and efficient results.
- Cost-Effective: A budget-friendly alternative to more expensive automatic scanners.
- Time-Saving: Reduces manual intervention, allowing you to focus on more critical tasks.
- Improved Workflow and Quality: Minimizes the risk of errors and inconsistencies, leading to better outcomes.
- User-Friendly Controls: Designed for ease of use, even for those with limited experience with microscopes.
For more information or placing an order, contact : sales@hs-analysis.com
Better workflow with HSA KIT
Comprehensive Slide Analysis with HS Analysis
At HS Analysis, we go beyond simple slide analysis. We integrate our solutions seamlessly into your existing infrastructure, ensuring that your Laboratory Information System (LIS) is connected and that slides are named for easy saving, searching, and medical use. Our goal is to provide a seamless experience, allowing you to access and utilize your data quickly and efficiently.
Traditional vs. AI-Powered Workflow
The traditional workflow of medical image analysis can be cumbersome. Typically, images from CT scans, MRIs, or X-rays are pre-processed and then analyzed by a radiologist. The radiologist evaluates the images and prepares a subjective report based on their expertise, often followed by a second opinion for quality assurance.
In contrast, AI-based analyses using HSA KIT offer a more streamlined and efficient approach:
- Standardized Process: Combines subjective and objective analysis for more consistent results.
- Feature Extraction: Identifies relevant features from raw data, creating meaningful representations for AI model training.
- User-Friendly Modules: Select and configure modules without excessive coding.
- Intuitive Software: Easy to learn, with capabilities to annotate, train, and automate processes.
- Efficient Image Analysis: Quickly analyzes multiple medical images, reducing the time needed for diagnosis and treatment.
- Automated Report Generation: Boosts productivity and assists physicians or radiologists in the evaluation process.
Seamless Integration with Laboratory Information Systems (LIS)
The HSA KIT software is designed to integrate effortlessly with existing Laboratory Information Systems (LIS), enabling smooth data exchange and interoperability. This integration streamlines your entire workflow—from sample collection to report generation—by minimizing manual data entry and reducing the risk of transcription errors. With real-time data synchronization between HSA KIT and your LIS, all relevant information is instantly accessible, ensuring a smooth and efficient diagnostic process.
Efficient Data Management with HSA Case Viewer
The HSA Case Viewer makes it easy to store and manage client files in a highly organized manner. Our smart data management system within HSA KIT provides structured data for case-based workflows, allowing users to quickly organize, analyze, and access the information they need.
Additionally, the advanced features of our system ensure data security and privacy, giving users confidence when handling sensitive information. With HSA KIT, you can streamline operations, improve efficiency, and maintain the highest standards of data integrity.
Powerful and Versatile Slide Analysis Software
At HS Analysis, we know how crucial accurate and efficient slide analysis is. That’s why our software is packed with features designed to help you achieve your goals effortlessly.
- Cross-Platform Compatibility: Our software runs smoothly on both Linux and Windows operating systems and is optimized for Docker. Whether you’re working online or offline, you have the flexibility to analyze slides without any interruptions.
- Seamless Integration: We offer professional integration into your network infrastructure, allowing our software to fit seamlessly into your existing systems.
- Interoperability: Designed to work with other programs, our software ensures that you have all the tools you need at your disposal.
- Optimized Performance: Even on less powerful computers, our software delivers top performance, enabling you to analyze slides quickly and accurately.
- Comprehensive Reporting: Generate detailed reports in CSV and Excel formats, giving you easy access to all the data you need.
- User Profile Management: Each user can save their history and preferences, ensuring a personalized and efficient workflow every time.
Trusted by Leading Companies, Hospitals, and Laboratories
In a short period of time, HS Analysis GmbH has built strong partnerships with numerous companies, hospitals, and laboratories. Our clients trust us to provide cutting-edge solutions for analyzing microscopic slides and data.
Using our HSA KIT software, physical slides can be easily digitized into Whole Slide Images (WSI), which can then be integrated with commonly used microscopes. The digitized data is readily available in the form of detailed reports and automated graphical representations, streamlining the analysis process and reducing the workload for medical professionals.
By simplifying and automating this traditionally extensive process, we help our clients save time and improve efficiency in their workflows.
AI-Powered Analysis: Enhancing, Not Replacing, Human Expertise
While AI-based analyses can significantly boost efficiency, it’s important to remember that AI serves as a powerful tool to support human expertise, not replace it. AI algorithms can sometimes produce false positives or negatives and may struggle with data that deviates from their training set.
At HS Analysis, we combine advanced technology with the expertise of our professional team to deliver exceptional slide analysis services tailored to your needs. Whether you require a one-time analysis or ongoing support, we have the tools and knowledge to help you achieve your goals with confidence.