HSA KIT: Precise Analysis of Hyphae and Vacuoles in Fungal Fermentation
Optimize your fungal fermentation processes with the Fungilyzer Module in HSA KIT, an advanced module based on pre-trained models that automatically detects and classifies hyphae and vacuoles. With our innovative technology, you can differentiate the hyphae of your fungal cultures into those with and without vacuoles, as well as into complex hyphae.
HSA KIT allows you to accurately track and visualize the development of hyphal count and area over various time points. With detailed and interactive plots, you gain deep insights into the growth dynamics of your fungal strains, helping you optimize your fermentation conditions.
Benefits of the Results:
- Growth Rate and Development Stage: Track the growth phases of your fungal cultures by monitoring hyphal count and area to determine the various developmental stages and respond early to changes.
- Nutrient Utilization and Metabolic Activity: Analyze the ratio of hyphae with and without vacuoles to draw conclusions about nutrient storage and metabolic processes, and maximize nutrient use efficiency.
- Stress Response and Adaptation: Detect stress conditions early by observing changes in vacuole formation and distribution within the hyphae, and adjust your fermentation conditions accordingly.
- Morphological Differentiation: Identify morphological changes and differentiation in the mycelium to make specific adjustments to the fermentation process and ensure the desired product quality.
Filamentous fungi are present in all types of ecosystems worldwide. They typically develop as a network of cells called hyphae. Organelles called vacuoles are responsible for nutrient storage and the breakdown of excess organelles. They secrete primary metabolites for their own metabolism, while secondary metabolites contribute to defense (antibiotics) or attachment (hydrophobins). As a result, various fungal species are of great importance in fields such as biotechnology, medicine, food production, and enzyme manufacturing.
The amazing AI-based analysis technology provided by HS Analysis GmbH is based on strategies that integrate objective analyses, utilizing facts and evidence to draw conclusions from data without using subjective viewpoints or biases, ensuring consistency and repeatability.
Preview of Hyphae and Vacuole Detection in HSA KIT: This advanced software enables the clear identification of viable structures, allowing for object detection in various complex spatial transformations.
However, merely identifying and analyzing specific structures in a complex process like fungal fermentation may not be sufficient. Despite numerous industrial applications, the process from cultivation to product extraction is very tedious, as the overgrown hyphae not only block sensors and lead to unreliable measurement results but also make the broth more viscous.
HSA KIT
The HSA KIT software features an intuitive user interface and professional high-end annotation capabilities to ensure pixel-perfect accuracy. By standardizing processes, maintaining consistency, and promoting reproducibility, it can enhance the entire analysis process.
The software focuses on object detection and identification, which are fundamental functions of standard image processing. Through image analysis, object detection algorithms identify and categorize objects of interest, providing useful data for further analysis and decision-making.
The FungiLyzer module focuses on detecting the two most important structures for studying fungal fermentation:
Hyphae: Long, thread-like structures (Red)
Vacuoles: Spherical structures; either separated or within the hyphae (Blue)
Absolute precision in detecting both structures. The object and background are easily distinguished by the model due to pixel-perfect classification training, which delineates the pixels within an image.
True Negatives
Hyphae with a white area inside are not of interest, as they may be growing under suboptimal conditions and are therefore less metabolically active.
Vacuoles consist of cell sap, which appears clear or transparent, so some white space in the middle is to be expected. A “completely dark” structure might indicate autophagy, for example.
Visualization issues related to the appearance of the structures could also arise. Therefore, the model would not recognize such structures for better training.
This is an enlarged view of the FungiLyzer model, which rejects background structures and only recognizes the required structures. The software is designed to remove noise and improve image resolution for highly precise object detection.
Below is a portion of a much larger image showing the truly outstanding object detection quality that the HSA KIT can achieve. The images below can be zoomed in and out, and there is a slider that can be moved from left to right to enhance the viewing experience.
Once the model is trained and the project is complete, the HS Analysis software provides the information needed to understand the results in a tabular format, including file names, number of objects (structures) such as hyphae and vacuoles, and the dimension of analyzed areas in square meters within a specific base ROI (Region of Interest) area.
The results sheet includes, but is not limited to, the basic information about the structures. In addition to these details, there are other specifics such as average area, perimeter, minimum and maximum diameter, etc.
While a base model provides a general or broad overview of the subject and offers a high level of understanding without delving into specific details or variations within the structures, the more customized module considers the various subtypes within each structure to ensure the results obtained are refined and more accurate.
In the image below, hyphae are further divided into three classes:
Without Vacuole: green
With Vacuole: orange
Complex: purple
Classify hyphae further into three subclasses. This provides an overview of the ongoing fermentation and helps to assume or identify the phase the process is in.
Biopesticides: Real-World Application
Biopesticides are derived from naturally occurring fungi and have proven to be successful in reducing damage caused by plant diseases, pests, or weeds to crops. Since they leave no toxic residues in the soil or water sources, fungal biopesticides are also a more environmentally friendly alternative to chemical pesticides. Furthermore, the fermentation process involves the use of renewable raw materials, i.e., glucose.
The FungiLyzer can detect anomalies or differences in the fermentation process by evaluating images of the process, enabling early intervention and avoiding potential inconsistencies in the process. This not only improves workflow efficiency but also minimizes the risk of economic losses for companies. The FungiLyzer also provides real-time data and insights that allow informed decisions and promote the optimization of culture processes for maximum efficiency.
Workflow with HSA KIT
Analyzing samples and digitizing slides has never been easier. HSA KIT offers its clients an unparalleled experience for those looking to keep pace with today’s “better” alternatives and achieve greater efficiency in their workflow. The HSA team goes all out to satisfy its customers, from installation and software integration to unlimited support and upgrades.
Standardized process with subjective/objective analysis
Extraction of relevant features from raw data and creation of meaningful representations for AI model training
Module selection and configuration without excessive coding
Easy-to-learn software: Annotate, Train, and Automate
Fast and efficient analysis of multiple medical images, reducing time for diagnosis or treatment
Automatic report generation to increase productivity and support doctors or radiologists in the evaluation process
We understand the importance of accurate and efficient slide analysis software. That’s why we offer a variety of features to help you achieve your goals.
Our software is compatible with both Linux and Windows operating systems and runs smoothly in Docker. With offline functionality, you can work on your slides without needing an internet connection, but if you want to expand to online use, that’s also possible.
We also offer professional integration into your network infrastructure, allowing you to seamlessly integrate our software into your existing systems.
Our software is designed to work with other programs, so you have all the tools you need at your disposal.
Even on weaker computers, our software delivers full performance, allowing you to analyze slides quickly and accurately.
And with the ability to generate reports in CSV and Excel formats, you have all the necessary data at your fingertips.
Finally, user profile management ensures that each user’s history and preferences are saved for easy access.
AI-based analyses can be much more efficient, but they can only serve as a supporting tool for human expertise and never a complete alternative. AI algorithms tend to produce false positives and false negatives and may struggle to adapt to data that deviates from the training datasets.
With our advanced technology and expert team, we are confident that we can deliver top-notch slide analysis services that meet the unique needs of each individual customer. Whether you are looking for a one-time analysis or continuous support, we have the tools and expertise required to help you achieve your goals.
Better than Alternative Software
Strong numerical computing programs can be used for data analysis, modeling, and simulation. While they have a wide range of industrial applications, there are several reasons why they may not be suitable for predicting scaling up in industrial processes.
- Limited Scalability: Most software programs are not designed to handle large industrial operations; they are more suited for small to medium tasks. For many industrial applications, scaling up the problem size can quickly become computationally expensive and time-consuming.
- Lack of Industry-Specific Tools: Despite the fact that there are general-purpose tools for data analysis, modeling, and simulation, they may not have the precise models and techniques needed to predict scaling up in industrial processes, such as those related to plant design, safety analysis, and process optimization.
- Limited Software Integration: Industrial processes often require a variety of software tools and platforms, and not all work perfectly with the programs and systems already used in the industry. This can make the modeling and simulation process inefficient and difficult to accurately predict scaling up.
- Insufficient Support for Parallel Computing: A single machine may not be able to handle the vast amounts of computing power required for many industrial processes. Some parallel computing capability may not be enough to meet the demands of simulations on an industrial scale.