Segmentation and Characterization of Macerated Fibers and Vessels Using Deep Learning

Purpose: Wood comprises different cell types, such as fibers and vessels, defining its properties. Studying their shape, size, and arrangement in microscopic images is crucial for understanding wood samples. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods. Results: In this work, we develop an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate fiber and vessel segmentation and characterization in microscopy images. The model can analyze 32640 x 25920 pixels images and demonstrate effective cell detection and segmentation, achieving a mAP_0.5-0.95 of 78 %. To assess the model's robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab. Conclusion: By leveraging YOLOv8's advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.

HI-Net: Hyperdense Inception 3D UNet for Brain Tumor Segmentation

The brain tumor segmentation task aims to classify tissue into the whole tumor (WT), tumor core (TC), and enhancing tumor (ET) classes using multimodel MRI images. Quantitative analysis of brain tumors is critical for clinical decision making. While manual segmentation is tedious, time-consuming, and subjective, this task is at the same time very challenging to automatic segmentation methods. Thanks to the powerful learning ability, convolutional neural networks (CNNs), mainly fully convolutional networks, have shown promising brain tumor segmentation. This paper further boosts the performance of brain tumor segmentation by proposing hyperdense inception 3D UNet (HI-Net), which captures multi-scale information by stacking factorization of 3D weighted convolutional layers in the residual inception block. We use hyper dense connections among factorized convolutional layers to extract more contexual information, with the help of features reusability. We use a dice loss function to cope with class imbalances. We validate the proposed architecture on the multi-modal brain tumor segmentation challenges (BRATS) 2020 testing dataset. Preliminary results on the BRATS 2020 testing set show that achieved by our proposed approach, the dice (DSC) scores of ET, WT, and TC are 0.79457, 0.87494, and 0.83712, respectively.

Context Aware 3D UNet for Brain Tumor Segmentation

Deep convolutional neural network (CNN) achieves remarkable performance for medical image analysis. UNet is the primary source in the performance of 3D CNN architectures for medical imaging tasks, including brain tumor segmentation. The skip connection in the UNet architecture concatenates features from both encoder and decoder paths to extract multi-contexual information from image data. The multi-scaled features play an essential role in brain tumor segmentation. However, the limited use of features can degrade the performance of the UNet approach for segmentation. In this paper, we propose a modified UNet architecture for brain tumor segmentation. In the proposed architecture, we used densely connected blocks in both encoder and decoder paths to extract multi-contexual information from the concept of feature reusability. The proposed residual inception blocks (RIB) are used to extract local and global information by merging features of different kernel sizes. We validate the proposed architecture on the multimodal brain tumor segmentation challenges (BRATS) 2020 testing dataset. The dice (DSC) scores of the whole tumor (WT), tumor core (TC), and enhancement tumor (ET) are 89.12%, 84.74%, and 79.12%, respectively. Our proposed work is in the top ten methods based on the dice scores of the testing dataset.