This content will become publicly available on February 1, 2025
Recent advancements in two-photon calcium imaging have enabled scientists to record the activity of thousands of neurons with cellular resolution. This scope of data collection is crucial to understanding the next generation of neuroscience questions, but analyzing these large recordings requires automated methods for neuron segmentation. Supervised methods for neuron segmentation achieve state of-the-art accuracy and speed but currently require large amounts of manually generated ground truth training labels. We reduced the required number of training labels by designing a semi-supervised pipeline. Our pipeline used neural network ensembling to generate pseudolabels to train a single shallow U-Net. We tested our method on three publicly available datasets and compared our performance to three widely used segmentation methods. Our method outperformed other methods when trained on a small number of ground truth labels and could achieve state-of-the-art accuracy after training on approximately a quarter of the number of ground truth labels as supervised methods. When trained on many ground truth labels, our pipeline attained higher accuracy than that of state-of-the-art methods. Overall, our work will help researchers accurately process large neural recordings while minimizing the time and effort needed to generate manual labels.
more » « less- Award ID(s):
- 1847540
- NSF-PAR ID:
- 10496102
- Publisher / Repository:
- Society for Neuroscience
- Date Published:
- Journal Name:
- eneuro
- Volume:
- 11
- Issue:
- 2
- ISSN:
- 2373-2822
- Page Range / eLocation ID:
- ENEURO.0352-23.2024
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract Objective. Recent advances in neural decoding have accelerated the development of brain–computer interfaces aimed at assisting users with everyday tasks such as speaking, walking, and manipulating objects. However, current approaches for training neural decoders commonly require large quantities of labeled data, which can be laborious or infeasible to obtain in real-world settings. Alternatively, self-supervised models that share self-generated pseudo-labels between two data streams have shown exceptional performance on unlabeled audio and video data, but it remains unclear how well they extend to neural decoding.Approach. We learn neural decoders without labels by leveraging multiple simultaneously recorded data streams, including neural, kinematic, and physiological signals. Specifically, we apply cross-modal, self-supervised deep clustering to train decoders that can classify movements from brain recordings. After training, we then isolate the decoders for each input data stream and compare the accuracy of decoders trained using cross-modal deep clustering against supervised and unimodal, self-supervised models.Main results. We find that sharing pseudo-labels between two data streams during training substantially increases decoding performance compared to unimodal, self-supervised models, with accuracies approaching those of supervised decoders trained on labeled data. Next, we extend cross-modal decoder training to three or more modalities, achieving state-of-the-art neural decoding accuracy that matches or slightly exceeds the performance of supervised models.Significance. We demonstrate that cross-modal, self-supervised decoding can be applied to train neural decoders when few or no labels are available and extend the cross-modal framework to share information among three or more data streams, further improving self-supervised training. -
more » « less
Network pruning is a widely used technique to reduce computation cost and model size for deep neural networks. However, the typical three-stage pipeline (i.e., training, pruning, and retraining (fine-tuning)) significantly increases the overall training time. In this article, we develop a systematic weight-pruning optimization approach based on surrogate Lagrangian relaxation (SLR), which is tailored to overcome difficulties caused by the discrete nature of the weight-pruning problem. We further prove that our method ensures fast convergence of the model compression problem, and the convergence of the SLR is accelerated by using quadratic penalties. Model parameters obtained by SLR during the training phase are much closer to their optimal values as compared to those obtained by other state-of-the-art methods. We evaluate our method on image classification tasks using CIFAR-10 and ImageNet with state-of-the-art multi-layer perceptron based networks such as MLP-Mixer; attention-based networks such as Swin Transformer; and convolutional neural network based models such as VGG-16, ResNet-18, ResNet-50, ResNet-110, and MobileNetV2. We also evaluate object detection and segmentation tasks on COCO, the KITTI benchmark, and the TuSimple lane detection dataset using a variety of models. Experimental results demonstrate that our SLR-based weight-pruning optimization approach achieves a higher compression rate than state-of-the-art methods under the same accuracy requirement and also can achieve higher accuracy under the same compression rate requirement. Under classification tasks, our SLR approach converges to the desired accuracy × faster on both of the datasets. Under object detection and segmentation tasks, SLR also converges 2× faster to the desired accuracy. Further, our SLR achieves high model accuracy even at the hardpruning stage without retraining, which reduces the traditional three-stage pruning into a two-stage process. Given a limited budget of retraining epochs, our approach quickly recovers the model’s accuracy.
-
In this paper, we present a novel terrain classifica- tion framework for large-scale remote sensing images. A well- performing multi-scale superpixel tessellation based segmentation approach is employed to generate homogeneous and irregularly shaped regions, and a transfer learning technique is sequentially deployed to derive representative deep features by utilizing suc- cessful pre-trained convolutional neural network (CNN) models. This design is aimed to overcome the big problem of lacking available ground-truth data and to increase the generalization power of the multi-pixel descriptor. In the subsequent classification step, we train a fast and robust support vector machine (SVM) to assign the pixel-level labels. Its maximum-margin property can be easily combined with a graph Laplacian propagation approach. Moreover, we analyze the advantages of applying a feature selection technique to the deep CNN features which are extracted by transfer learning. In the experiments, we evaluate the whole framework based on different geographical types. Compared with other region-based classification methods, the results show that our framework can obtain state-of-the-art performance w.r.t. both classification accuracy and computational efficiency.more » « less
-
Stereology-based methods provide the current state-of-the-art approaches for accurate quantification of numbers and other morphometric parameters of biological objects in stained tissue sections. The advent of artificial intelligence (AI)-based deep learning (DL) offers the possibility of improving throughput by automating the collection of stereology data. We have recently shown that DL can effectively achieve comparable accuracy to manual stereology but with higher repeatability, improved throughput, and less variation due to human factors by quantifying the total number of immunostained cells at their maximal profile of focus in extended depth of field (EDF) images. In the first of two novel contributions in this work, we propose a semi-automatic approach using a handcrafted Adaptive Segmentation Algorithm (ASA) to automatically generate ground truth on EDF images for training our deep learning (DL) models to automatically count cells using unbiased stereology methods. This update increases the amount of training data, thereby improving the accuracy and efficiency of automatic cell counting methods, without a requirement for extra expert time. The second contribution of this work is a Multi-channel Input and Multi-channel Output (MIMO) method using a U-Net deep learning architecture for automatic cell counting in a stack of z-axis images (also known as disector stacks). This DL-based digital automation of the ordinary optical fractionator ensures accurate counts through spatial separation of stained cells in the z-plane, thereby avoiding false negatives from overlapping cells in EDF images without the shortcomings of 3D and recurrent DL models. The contribution overcomes the issue of under-counting errors with EDF images due to overlapping cells in the z-plane (masking). We demonstrate the practical applications of these advances with automatic disector-based estimates of the total number of NeuN-immunostained neurons in a mouse neocortex. In summary, this work provides the first demonstration of automatic estimation of a total cell number in tissue sections using a combination of deep learning and the disector-based optical fractionator method.more » « less
-
null (Ed.)The success of supervised learning requires large-scale ground truth labels which are very expensive, time- consuming, or may need special skills to annotate. To address this issue, many self- or un-supervised methods are developed. Unlike most existing self-supervised methods to learn only 2D image features or only 3D point cloud features, this paper presents a novel and effective self-supervised learning approach to jointly learn both 2D image features and 3D point cloud features by exploiting cross-modality and cross-view correspondences without using any human annotated labels. Specifically, 2D image features of rendered images from different views are extracted by a 2D convolutional neural network, and 3D point cloud features are extracted by a graph convolution neural network. Two types of features are fed into a two-layer fully connected neural network to estimate the cross-modality correspondence. The three networks are jointly trained (i.e. cross-modality) by verifying whether two sampled data of different modalities belong to the same object, meanwhile, the 2D convolutional neural network is additionally optimized through minimizing intra-object distance while maximizing inter-object distance of rendered images in different views (i.e. cross-view). The effectiveness of the learned 2D and 3D features is evaluated by transferring them on five different tasks including multi-view 2D shape recognition, 3D shape recognition, multi-view 2D shape retrieval, 3D shape retrieval, and 3D part-segmentation. Extensive evaluations on all the five different tasks across different datasets demonstrate strong generalization and effectiveness of the learned 2D and 3D features by the proposed self-supervised method.more » « less
