Hey everyone!
\nI wanted to start a papers thread and build on it, and hope others share as well, papers to gain domain knowledge. I have no domain knowledge in this area so I have downloaded papers that appeared to be relevant after reading their abstracts. I'll be reading these over the coming days and commenting more as I go through all of them. Hope this helps!
\nResearch Papers:
\nFeedback U-net for Cell Image Segmentation - Human brain is a layered structure, and performs not only a feedforward process from a lower layer to an upper layer but also a feedback process from an upper layer to a lower layer. The layer is a collection of neurons, and neural network is a mathematical model of the function of neurons. Although neural network imitates the human brain, everyone uses only feedforward process from the lower layer to the upper layer, and feedback process from the upper layer to the lower layer is not used. Therefore, in this paper, we propose Feedback U-Net using Convolutional LSTM which is the segmentation method using Convolutional LSTM and feedback process. The output of U-net gave feedback to the input, and the second round is performed. By using Convolutional LSTM, the features in the second round are extracted based on the features acquired in the first round. On both of the Drosophila cell image and Mouse cell image datasets, our method outperformed conventional U-Net which uses only feedforward process.
Efficient 2D neuron boundary segmentation with local topological constraints - Drawing inspiration from these human strategies, we formulate the segmentation task as an edge labeling problem on a graph with local topological constraints. We derive an integer linear program (ILP) that enforces membrane continuity, i.e. the absence of gaps. The cost function of the ILP is the pixel-wise deviation of the segmentation from a priori membrane probabilities derived from the data.
\nBased on membrane probability maps obtained using random forest classifiers and convolutional neural networks, our method improves the neuron boundary segmentation accuracy compared to a variety of standard segmentation approaches. Our method successfully performs gap completion and leads to fewer topological errors. The method could potentially also be incorporated into other image segmentation pipelines with known topological constraints.
Contrastive Representation Learning for Whole Brain Cytoarchitectonic Mapping in Histological Human Brain Sections - Cytoarchitectonic maps provide microstructural reference parcellations of the brain, describing its organization in terms of the spatial arrangement of neuronal cell bodies as measured from histological tissue sections. Recent work provided the first automatic segmentations of cytoarchitectonic areas in the visual system using Convolutional Neural Networks. We aim to extend this approach to become applicable to a wider range of brain areas, envisioning a solution for mapping the complete human brain. Inspired by recent success in image classification, we propose a contrastive learning objective for encoding microscopic image patches into robust microstructural features, which are efficient for cytoarchitectonic area classification. We show that a model pre-trained using this learning task outperforms a model trained from scratch, as well as a model pre-trained on a recently proposed auxiliary task. We perform cluster analysis in the feature space to show that the learned representations form anatomically meaningful groups.
A Novel Neuron Model of Visual Processor - Our model inherited the threshold exponential decay and synchronous pulse oscillation property of the original PCNN model, and it can exhibit chaotic behavior consistent with the testing results of cat primary visual cortex neurons. Therefore, our CCNN model is closer to real visual neural networks. For image segmentation tasks, the algorithm based on CCNN model has better performance than the state-of-art of visual cortex neural network model. The strength of our approach is that it helps neurophysiologists further understand how the primary visual cortex works and can be used to quantitatively predict the temporal-spatial behavior of real neural networks. CCNN may also inspire engineers to create brain-inspired deep learning networks for artificial intelligence purposes.
VICE: Visual Identification and Correction of Neural Circuit Errors - This paper presents the design and implementation of an analytics framework that streamlines proofreading, focusing on connectivity-related errors. We accomplish this with automated likely-error detection and synapse clustering that drives the proofreading effort with highly interactive 3D visualizations. In particular, our strategy centers on proofreading the local circuit of a single cell to ensure a basic level of completeness. We demonstrate our framework's utility with a user study and report quantitative and subjective feedback from our users. Overall, users find the framework more efficient for proofreading, understanding evolving graphs, and sharing error correction strategies.
Hidden Markov Modeling for Maximum Likelihood Neuron Reconstruction - Recent advances in brain clearing and imaging have made it possible to image entire mammalian brains at sub-micron resolution. These images offer the potential to assemble brain-wide atlases of projection neuron morphology, but manual neuron reconstruction remains a bottleneck. In this paper we present a probabilistic method which combines a hidden Markov state process that encodes neuron geometric properties with a random field appearance model of the flourescence process.
Hey everyone!
\nI wanted to start a papers thread and build on it, and hope others share as well, papers to gain domain knowledge. I have no domain knowledge in this area so I have downloaded papers that appeared to be relevant after reading their abstracts. I'll be reading these over the coming days and commenting more as I go through all of them. Hope this helps!
\nResearch Papers:
\nFeedback U-net for Cell Image Segmentation - Human brain is a layered structure, and performs not only a feedforward process from a lower layer to an upper layer but also a feedback process from an upper layer to a lower layer. The layer is a collection of neurons, and neural network is a mathematical model of the function of neurons. Although neural network imitates the human brain, everyone uses only feedforward process from the lower layer to the upper layer, and feedback process from the upper layer to the lower layer is not used. Therefore, in this paper, we propose Feedback U-Net using Convolutional LSTM which is the segmentation method using Convolutional LSTM and feedback process. The output of U-net gave feedback to the input, and the second round is performed. By using Convolutional LSTM, the features in the second round are extracted based on the features acquired in the first round. On both of the Drosophila cell image and Mouse cell image datasets, our method outperformed conventional U-Net which uses only feedforward process.
Efficient 2D neuron boundary segmentation with local topological constraints - Drawing inspiration from these human strategies, we formulate the segmentation task as an edge labeling problem on a graph with local topological constraints. We derive an integer linear program (ILP) that enforces membrane continuity, i.e. the absence of gaps. The cost function of the ILP is the pixel-wise deviation of the segmentation from a priori membrane probabilities derived from the data.
\nBased on membrane probability maps obtained using random forest classifiers and convolutional neural networks, our method improves the neuron boundary segmentation accuracy compared to a variety of standard segmentation approaches. Our method successfully performs gap completion and leads to fewer topological errors. The method could potentially also be incorporated into other image segmentation pipelines with known topological constraints.
Contrastive Representation Learning for Whole Brain Cytoarchitectonic Mapping in Histological Human Brain Sections - Cytoarchitectonic maps provide microstructural reference parcellations of the brain, describing its organization in terms of the spatial arrangement of neuronal cell bodies as measured from histological tissue sections. Recent work provided the first automatic segmentations of cytoarchitectonic areas in the visual system using Convolutional Neural Networks. We aim to extend this approach to become applicable to a wider range of brain areas, envisioning a solution for mapping the complete human brain. Inspired by recent success in image classification, we propose a contrastive learning objective for encoding microscopic image patches into robust microstructural features, which are efficient for cytoarchitectonic area classification. We show that a model pre-trained using this learning task outperforms a model trained from scratch, as well as a model pre-trained on a recently proposed auxiliary task. We perform cluster analysis in the feature space to show that the learned representations form anatomically meaningful groups.
A Novel Neuron Model of Visual Processor - Our model inherited the threshold exponential decay and synchronous pulse oscillation property of the original PCNN model, and it can exhibit chaotic behavior consistent with the testing results of cat primary visual cortex neurons. Therefore, our CCNN model is closer to real visual neural networks. For image segmentation tasks, the algorithm based on CCNN model has better performance than the state-of-art of visual cortex neural network model. The strength of our approach is that it helps neurophysiologists further understand how the primary visual cortex works and can be used to quantitatively predict the temporal-spatial behavior of real neural networks. CCNN may also inspire engineers to create brain-inspired deep learning networks for artificial intelligence purposes.
VICE: Visual Identification and Correction of Neural Circuit Errors - This paper presents the design and implementation of an analytics framework that streamlines proofreading, focusing on connectivity-related errors. We accomplish this with automated likely-error detection and synapse clustering that drives the proofreading effort with highly interactive 3D visualizations. In particular, our strategy centers on proofreading the local circuit of a single cell to ensure a basic level of completeness. We demonstrate our framework's utility with a user study and report quantitative and subjective feedback from our users. Overall, users find the framework more efficient for proofreading, understanding evolving graphs, and sharing error correction strategies.
Hidden Markov Modeling for Maximum Likelihood Neuron Reconstruction - Recent advances in brain clearing and imaging have made it possible to image entire mammalian brains at sub-micron resolution. These images offer the potential to assemble brain-wide atlases of projection neuron morphology, but manual neuron reconstruction remains a bottleneck. In this paper we present a probabilistic method which combines a hidden Markov state process that encodes neuron geometric properties with a random field appearance model of the flourescence process.
great article.
", "rawMarkdown": "great article.", "votes": null } ], "comments": [ { "id": 3177802, "author_name": "sherazbaloch", "author_url": "", "post_date": "04/13/2025 09:52:41", "content": "great article.
", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "1547701": "Hey everyone!\n\nI wanted to start a papers thread and build on it, and hope others share as well, papers to gain domain knowledge. I have no domain knowledge in this area so I have downloaded papers that appeared to be relevant after reading their abstracts. I'll be reading these over the coming days and commenting more as I go through all of them. Hope this helps!\n\n**Research Papers:**\n\n- [Feedback U-net for Cell Image Segmentation](https://arxiv.org/abs/2004.14581) - Human brain is a layered structure, and performs not only a feedforward process from a lower layer to an upper layer but also a feedback process from an upper layer to a lower layer. The layer is a collection of neurons, and neural network is a mathematical model of the function of neurons. Although neural network imitates the human brain, everyone uses only feedforward process from the lower layer to the upper layer, and feedback process from the upper layer to the lower layer is not used. Therefore, in this paper, we propose Feedback U-Net using Convolutional LSTM which is the segmentation method using Convolutional LSTM and feedback process. The output of U-net gave feedback to the input, and the second round is performed. By using Convolutional LSTM, the features in the second round are extracted based on the features acquired in the first round. On both of the Drosophila cell image and Mouse cell image datasets, our method outperformed conventional U-Net which uses only feedforward process.\n\n- [Efficient 2D neuron boundary segmentation with local topological constraints](https://arxiv.org/abs/2002.01036) - Drawing inspiration from these human strategies, we formulate the segmentation task as an edge labeling problem on a graph with local topological constraints. We derive an integer linear program (ILP) that enforces membrane continuity, i.e. the absence of gaps. The cost function of the ILP is the pixel-wise deviation of the segmentation from a priori membrane probabilities derived from the data.\nBased on membrane probability maps obtained using random forest classifiers and convolutional neural networks, our method improves the neuron boundary segmentation accuracy compared to a variety of standard segmentation approaches. Our method successfully performs gap completion and leads to fewer topological errors. The method could potentially also be incorporated into other image segmentation pipelines with known topological constraints.\n\n- [Contrastive Representation Learning for Whole Brain Cytoarchitectonic Mapping in Histological Human Brain Sections](https://arxiv.org/abs/2011.12865) - Cytoarchitectonic maps provide microstructural reference parcellations of the brain, describing its organization in terms of the spatial arrangement of neuronal cell bodies as measured from histological tissue sections. Recent work provided the first automatic segmentations of cytoarchitectonic areas in the visual system using Convolutional Neural Networks. We aim to extend this approach to become applicable to a wider range of brain areas, envisioning a solution for mapping the complete human brain. Inspired by recent success in image classification, we propose a contrastive learning objective for encoding microscopic image patches into robust microstructural features, which are efficient for cytoarchitectonic area classification. We show that a model pre-trained using this learning task outperforms a model trained from scratch, as well as a model pre-trained on a recently proposed auxiliary task. We perform cluster analysis in the feature space to show that the learned representations form anatomically meaningful groups.\n\n- [A Novel Neuron Model of Visual Processor](https://arxiv.org/abs/2104.07257) - Our model inherited the threshold exponential decay and synchronous pulse oscillation property of the original PCNN model, and it can exhibit chaotic behavior consistent with the testing results of cat primary visual cortex neurons. Therefore, our CCNN model is closer to real visual neural networks. For image segmentation tasks, the algorithm based on CCNN model has better performance than the state-of-art of visual cortex neural network model. The strength of our approach is that it helps neurophysiologists further understand how the primary visual cortex works and can be used to quantitatively predict the temporal-spatial behavior of real neural networks. CCNN may also inspire engineers to create brain-inspired deep learning networks for artificial intelligence purposes.\n\n- [VICE: Visual Identification and Correction of Neural Circuit Errors](https://arxiv.org/abs/2105.06861) - This paper presents the design and implementation of an analytics framework that streamlines proofreading, focusing on connectivity-related errors. We accomplish this with automated likely-error detection and synapse clustering that drives the proofreading effort with highly interactive 3D visualizations. In particular, our strategy centers on proofreading the local circuit of a single cell to ensure a basic level of completeness. We demonstrate our framework's utility with a user study and report quantitative and subjective feedback from our users. Overall, users find the framework more efficient for proofreading, understanding evolving graphs, and sharing error correction strategies.\n\n- [Hidden Markov Modeling for Maximum Likelihood Neuron Reconstruction](https://arxiv.org/abs/2106.02701) - Recent advances in brain clearing and imaging have made it possible to image entire mammalian brains at sub-micron resolution. These images offer the potential to assemble brain-wide atlases of projection neuron morphology, but manual neuron reconstruction remains a bottleneck. In this paper we present a probabilistic method which combines a hidden Markov state process that encodes neuron geometric properties with a random field appearance model of the flourescence process.", "3177802": "great article." }, "source": "meta" }