Search Results for author: Jeff W. Lichtman

Found 11 papers, 3 papers with code

VICE: Visual Identification and Correction of Neural Circuit Errors

no code implementations14 May 2021 Felix Gonda, Xueying Wang, Johanna Beyer, Markus Hadwiger, Jeff W. Lichtman, Hanspeter Pfister

A connectivity graph of neurons at the resolution of single synapses provides scientists with a tool for understanding the nervous system in health and disease.

Semantic Segmentation

Learning Guided Electron Microscopy with Active Acquisition

1 code implementation7 Jan 2021 Lu Mi, Hao Wang, Yaron Meirovitch, Richard Schalek, Srinivas C. Turaga, Jeff W. Lichtman, Aravinthan D. T. Samuel, Nir Shavit

Single-beam scanning electron microscopes (SEM) are widely used to acquire massive data sets for biomedical study, material analysis, and fabrication inspection.

A Topological Nomenclature for 3D Shape Analysis in Connectomics

1 code implementation27 Sep 2019 Abhimanyu Talwar, Zudi Lin, Donglai Wei, Yuesong Wu, Bowen Zheng, Jinglin Zhao, Won-Dong Jang, Xueying Wang, Jeff W. Lichtman, Hanspeter Pfister

Next, we develop nomenclature rules for pyramidal neurons and mitochondria from the reduced graph and finally learn the feature embedding for shape manipulation.

3D Shape Classification 3D Shape Retrieval

Detecting Synapse Location and Connectivity by Signed Proximity Estimation and Pruning with Deep Nets

1 code implementation8 Jul 2018 Toufiq Parag, Daniel Berger, Lee Kamentsky, Benedikt Staffler, Donglai Wei, Moritz Helmstaedter, Jeff W. Lichtman, Hanspeter Pfister

The few methods that computes direction along with contact location have only been demonstrated to work on either dyadic (most common in vertebrate brain) or polyadic (found in fruit fly brain) synapses, but not on both types.

Anisotropic EM Segmentation by 3D Affinity Learning and Agglomeration

no code implementations27 Jul 2017 Toufiq Parag, Fabian Tschopp, William Grisaitis, Srinivas C. Turaga, Xuewen Zhang, Brian Matejek, Lee Kamentsky, Jeff W. Lichtman, Hanspeter Pfister

The field of connectomics has recently produced neuron wiring diagrams from relatively large brain regions from multiple animals.

Guided Proofreading of Automatic Segmentations for Connectomics

no code implementations CVPR 2018 Daniel Haehn, Verena Kaynig, James Tompkin, Jeff W. Lichtman, Hanspeter Pfister

Automatic cell image segmentation methods in connectomics produce merge and split errors, which require correction through proofreading.

Semantic Segmentation

Registering large volume serial-section electron microscopy image sets for neural circuit reconstruction using FFT signal whitening

no code implementations14 Dec 2016 Arthur W. Wetzel, Jennifer Bakal, Markus Dittrich, David G. C. Hildebrand, Josh L. Morgan, Jeff W. Lichtman

The detailed reconstruction of neural anatomy for connectomics studies requires a combination of resolution and large three-dimensional data capture provided by serial section electron microscopy (ssEM).

Image Registration

RhoanaNet Pipeline: Dense Automatic Neural Annotation

no code implementations21 Nov 2016 Seymour Knowles-Barley, Verena Kaynig, Thouis Ray Jones, Alyssa Wilson, Joshua Morgan, Dongil Lee, Daniel Berger, Narayanan Kasthuri, Jeff W. Lichtman, Hanspeter Pfister

The best segmentation results obtained gave $V^\text{Info}_\text{F-score}$ scores of 0. 9054 and 09182 for the cortex datasets, 0. 9438 for LGN, and 0. 9150 for Cerebellum.

Automatic Annotation of Axoplasmic Reticula in Pursuit of Connectomes

no code implementations16 Apr 2014 Ayushi Sinha, William Gray Roncal, Narayanan Kasthuri, Ming Chuang, Priya Manavalan, Dean M. Kleissas, Joshua T. Vogelstein, R. Jacob Vogelstein, Randal Burns, Jeff W. Lichtman, Michael Kazhdan

The contribution of this work is the introduction of a straightforward and robust pipeline which annotates axoplasmic reticula with high precision, contributing towards advancements in automatic feature annotations in neural EM data.

Automatic Annotation of Axoplasmic Reticula in Pursuit of Connectomes using High-Resolution Neural EM Data

no code implementations16 Apr 2014 Ayushi Sinha, William Gray Roncal, Narayanan Kasthuri, Jeff W. Lichtman, Randal Burns, Michael Kazhdan

Accurately estimating the wiring diagram of a brain, known as a connectome, at an ultrastructure level is an open research problem.

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