Test-Time Adaptation with SaLIP: A Cascade of SAM and CLIP for Zero shot Medical Image Segmentation

The Segment Anything Model (SAM) and CLIP are remarkable vision foundation models (VFMs). SAM, a prompt driven segmentation model, excels in segmentation tasks across diverse domains, while CLIP is renowned for its zero shot recognition capabilities. However, their unified potential has not yet been explored in medical image segmentation. To adapt SAM to medical imaging, existing methods primarily rely on tuning strategies that require extensive data or prior prompts tailored to the specific task, making it particularly challenging when only a limited number of data samples are available. This work presents an in depth exploration of integrating SAM and CLIP into a unified framework for medical image segmentation. Specifically, we propose a simple unified framework, SaLIP, for organ segmentation. Initially, SAM is used for part based segmentation within the image, followed by CLIP to retrieve the mask corresponding to the region of interest (ROI) from the pool of SAM generated masks. Finally, SAM is prompted by the retrieved ROI to segment a specific organ. Thus, SaLIP is training and fine tuning free and does not rely on domain expertise or labeled data for prompt engineering. Our method shows substantial enhancements in zero shot segmentation, showcasing notable improvements in DICE scores across diverse segmentation tasks like brain (63.46%), lung (50.11%), and fetal head (30.82%), when compared to un prompted SAM. Code and text prompts will be available online.

MiTU-Net: A fine-tuned U-Net with SegFormer backbone for segmenting pubic symphysis-fetal head

Ultrasound measurements have been examined as potential tools for predicting the likelihood of successful vaginal delivery. The angle of progression (AoP) is a measurable parameter that can be obtained during the initial stage of labor. The AoP is defined as the angle between a straight line along the longitudinal axis of the pubic symphysis (PS) and a line from the inferior edge of the PS to the leading edge of the fetal head (FH). However, the process of measuring AoP on ultrasound images is time consuming and prone to errors. To address this challenge, we propose the Mix Transformer U-Net (MiTU-Net) network, for automatic fetal head-pubic symphysis segmentation and AoP measurement. The MiTU-Net model is based on an encoder-decoder framework, utilizing a pre-trained efficient transformer to enhance feature representation. Within the efficient transformer encoder, the model significantly reduces the trainable parameters of the encoder-decoder model. The effectiveness of the proposed method is demonstrated through experiments conducted on a recent transperineal ultrasound dataset. Our model achieves competitive performance, ranking 5th compared to existing approaches. The MiTU-Net presents an efficient method for automatic segmentation and AoP measurement, reducing errors and assisting sonographers in clinical practice. Reproducibility: Framework implementation and models available on https://github.com/13204942/MiTU-Net.

Lightweight Framework for Automated Kidney Stone Detection using coronal CT images

Kidney stone disease results in millions of annual visits to emergency departments in the United States. Computed tomography (CT) scans serve as the standard imaging modality for efficient detection of kidney stones. Various approaches utilizing convolutional neural networks (CNNs) have been proposed to implement automatic diagnosis of kidney stones. However, there is a growing interest in employing fast and efficient CNNs on edge devices in clinical practice. In this paper, we propose a lightweight fusion framework for kidney detection and kidney stone diagnosis on coronal CT images. In our design, we aim to minimize the computational costs of training and inference while implementing an automated approach. The experimental results indicate that our framework can achieve competitive outcomes using only 8\% of the original training data. These results include an F1 score of 96\% and a False Negative (FN) error rate of 4\%. Additionally, the average detection time per CT image on a CPU is 0.62 seconds. Reproducibility: Framework implementation and models available on GitHub.

Novel Models for Multiple Dependent Heteroskedastic Time Series

Functional magnetic resonance imaging or functional MRI (fMRI) is a very popular tool used for differing brain regions by measuring brain activity. It is affected by physiological noise, such as head and brain movement in the scanner from breathing, heart beats, or the subject fidgeting. The purpose of this paper is to propose a novel approach to handling fMRI data for infants with high volatility caused by sudden head movements. Another purpose is to evaluate the volatility modelling performance of multiple dependent fMRI time series data. The models examined in this paper are AR and GARCH and the modelling performance is evaluated by several statistical performance measures. The conclusions of this paper are that multiple dependent fMRI series data can be fitted with AR + GARCH model if the multiple fMRI data have many sudden head movements. The GARCH model can capture the shared volatility clustering caused by head movements across brain regions. However, the multiple fMRI data without many head movements have fitted AR + GARCH model with different performance. The conclusions are supported by statistical tests and measures. This paper highlights the difference between the proposed approach from traditional approaches when estimating model parameters and modelling conditional variances on multiple dependent time series. In the future, the proposed approach can be applied to other research fields, such as financial economics, and signal processing. Code is available at \url{https://github.com/13204942/STAT40710}.

Evaluate Fine-tuning Strategies for Fetal Head Ultrasound Image Segmentation with U-Net

Fetal head segmentation is a crucial step in measuring the fetal head circumference (HC) during gestation, an important biometric in obstetrics for monitoring fetal growth. However, manual biometry generation is time-consuming and results in inconsistent accuracy. To address this issue, convolutional neural network (CNN) models have been utilized to improve the efficiency of medical biometry. But training a CNN network from scratch is a challenging task, we proposed a Transfer Learning (TL) method. Our approach involves fine-tuning (FT) a U-Net network with a lightweight MobileNet as the encoder to perform segmentation on a set of fetal head ultrasound (US) images with limited effort. This method addresses the challenges associated with training a CNN network from scratch. It suggests that our proposed FT strategy yields segmentation performance that is comparable when trained with a reduced number of parameters by 85.8%. And our proposed FT strategy outperforms other strategies with smaller trainable parameter sizes below 4.4 million. Thus, we contend that it can serve as a dependable FT approach for reducing the size of models in medical image analysis. Our key findings highlight the importance of the balance between model performance and size in developing Artificial Intelligence (AI) applications by TL methods. Code is available at https://github.com/13204942/FT_Methods_for_Fetal_Head_Segmentation.