NeuReg: Domain-invariant 3D Image Registration on Human and Mouse Brains

Medical brain imaging relies heavily on image registration to accurately curate structural boundaries of brain features for various healthcare applications. Deep learning models have shown remarkable performance in image registration in recent years. Still, they often struggle to handle the diversity of 3D brain volumes, challenged by their structural and contrastive variations and their imaging domains. In this work, we present NeuReg, a Neuro-inspired 3D image registration architecture with the feature of domain invariance. NeuReg generates domain-agnostic representations of imaging features and incorporates a shifting window-based Swin Transformer block as the encoder. This enables our model to capture the variations across brain imaging modalities and species. We demonstrate a new benchmark in multi-domain publicly available datasets comprising human and mouse 3D brain volumes. Extensive experiments reveal that our model (NeuReg) outperforms the existing baseline deep learning-based image registration models and provides a high-performance boost on cross-domain datasets, where models are trained on 'source-only' domain and tested on completely 'unseen' target domains. Our work establishes a new state-of-the-art for domain-agnostic 3D brain image registration, underpinned by Neuro-inspired Transformer-based architecture.

AnimalFormer: Multimodal Vision Framework for Behavior-based Precision Livestock Farming

We introduce a multimodal vision framework for precision livestock farming, harnessing the power of GroundingDINO, HQSAM, and ViTPose models. This integrated suite enables comprehensive behavioral analytics from video data without invasive animal tagging. GroundingDINO generates accurate bounding boxes around livestock, while HQSAM segments individual animals within these boxes. ViTPose estimates key body points, facilitating posture and movement analysis. Demonstrated on a sheep dataset with grazing, running, sitting, standing, and walking activities, our framework extracts invaluable insights: activity and grazing patterns, interaction dynamics, and detailed postural evaluations. Applicable across species and video resolutions, this framework revolutionizes non-invasive livestock monitoring for activity detection, counting, health assessments, and posture analyses. It empowers data-driven farm management, optimizing animal welfare and productivity through AI-powered behavioral understanding.

A comparison of automatic multi-tissue segmentation methods of the human fetal brain using the FeTA Dataset

It is critical to quantitatively analyse the developing human fetal brain in order to fully understand neurodevelopment in both normal fetuses and those with congenital disorders. To facilitate this analysis, automatic multi-tissue fetal brain segmentation algorithms are needed, which in turn requires open databases of segmented fetal brains. Here we introduce a publicly available database of 50 manually segmented pathological and non-pathological fetal magnetic resonance brain volume reconstructions across a range of gestational ages (20 to 33 weeks) into 7 different tissue categories (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, deep grey matter, brainstem/spinal cord). In addition, we quantitatively evaluate the accuracy of several automatic multi-tissue segmentation algorithms of the developing human fetal brain. Four research groups participated, submitting a total of 10 algorithms, demonstrating the benefits the database for the development of automatic algorithms.

Exploring Intensity Invariance in Deep Neural Networks for Brain Image Registration

Image registration is a widely-used technique in analysing large scale datasets that are captured through various imaging modalities and techniques in biomedical imaging such as MRI, X-Rays, etc. These datasets are typically collected from various sites and under different imaging protocols using a variety of scanners. Such heterogeneity in the data collection process causes inhomogeneity or variation in intensity (brightness) and noise distribution. These variations play a detrimental role in the performance of image registration, segmentation and detection algorithms. Classical image registration methods are computationally expensive but are able to handle these artifacts relatively better. However, deep learning-based techniques are shown to be computationally efficient for automated brain registration but are sensitive to the intensity variations. In this study, we investigate the effect of variation in intensity distribution among input image pairs for deep learning-based image registration methods. We find a performance degradation of these models when brain image pairs with different intensity distribution are presented even with similar structures. To overcome this limitation, we incorporate a structural similarity-based loss function in a deep neural network and test its performance on the validation split separated before training as well as on a completely unseen new dataset. We report that the deep learning models trained with structure similarity-based loss seems to perform better for both datasets. This investigation highlights a possible performance limiting factor in deep learning-based registration models and suggests a potential solution to incorporate the intensity distribution variation in the input image pairs. Our code and models are available at https://github.com/hassaanmahmood/DeepIntense.

Decoding Neural Responses in Mouse Visual Cortex through a Deep Neural Network

Finding a code to unravel the population of neural responses that leads to a distinct animal behavior has been a long-standing question in the field of neuroscience. With the recent advances in machine learning, it is shown that the hierarchically Deep Neural Networks (DNNs) perform optimally in decoding unique features out of complex datasets. In this study, we utilize the power of a DNN to explore the computational principles in the mammalian brain by exploiting the Neuropixel data from Allen Brain Institute. We decode the neural responses from mouse visual cortex to predict the presented stimuli to the animal for natural (bear, trees, cheetah, etc.) and artificial (drifted gratings, orientated bars, etc.) classes. Our results indicate that neurons in mouse visual cortex encode the features of natural and artificial objects in a distinct manner, and such neural code is consistent across animals. We investigate this by applying transfer learning to train a DNN on the neural responses of a single animal and test its generalized performance across multiple animals. Within a single animal, DNN is able to decode the neural responses with as much as 100% classification accuracy. Across animals, this accuracy is reduced to 91%. This study demonstrates the potential of utilizing the DNN models as a computational framework to understand the neural coding principles in the mammalian brain.

Developing Brain Atlas through Deep Learning

To uncover the organizational principles governing the human brain, neuroscientists are in need of developing high-throughput methods that can explore the structure and function of distinct brain regions using animal models. The first step towards this goal is to accurately register the regions of interest in a mouse brain, against a standard reference atlas, with minimum human supervision. The second step is to scale this approach to different animal ages, so as to also allow insights into normal and pathological brain development and aging. We introduce here a fully automated convolutional neural network-based method (SeBRe) for registration through Segmenting Brain Regions of interest in mice at different ages. We demonstrate the validity of our method on different mouse brain post-natal (P) developmental time points, across a range of neuronal markers. Our method outperforms the existing brain registration methods, and provides the minimum mean squared error (MSE) score on a mouse brain dataset. We propose that our deep learning-based registration method can (i) accelerate brain-wide exploration of region-specific changes in brain development and (ii) replace the existing complex brain registration methodology, by simply segmenting brain regions of interest for high-throughput brain-wide analysis.

Exploring Brain-wide Development of Inhibition through Deep Learning

We introduce here a fully automated convolutional neural network-based method for brain image processing to Detect Neurons in different brain Regions during Development (DeNeRD). Our method takes a developing mouse brain as input and i) registers the brain sections against a developing mouse reference atlas, ii) detects various types of neurons, and iii) quantifies the neural density in many unique brain regions at different postnatal (P) time points. Our method is invariant to the shape, size and expression of neurons and by using DeNeRD, we compare the brain-wide neural density of all GABAergic neurons in developing brains of ages P4, P14 and P56. We discover and report 6 different clusters of regions in the mouse brain in which GABAergic neurons develop in a differential manner from early age (P4) to adulthood (P56). These clusters reveal key steps of GABAergic cell development that seem to track with the functional development of diverse brain regions as the mouse transitions from a passive receiver of sensory information (<P14) to an active seeker (>P14).