skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Attention:

The NSF Public Access Repository (PAR) system and access will be unavailable from 11:00 PM ET on Friday, May 16 until 2:00 AM ET on Saturday, May 17 due to maintenance. We apologize for the inconvenience.


Title: Tree Instance Segmentation with Temporal Contour Graph
We present a novel approach to perform instance segmentation and counting for densely packed self-similar trees using a top-view RGB image sequence. We propose a solution that leverages pixel content, shape, and self-occlusion. First, we perform an initial over-segmentation of the image sequence and aggregate structural characteristics into a contour graph with temporal information incorporated. Second, using a graph convolutional network and its inherent local messaging passing abilities, we merge adjacent tree crown patches into a final set of tree crowns. Per various studies and comparisons, our method is superior to all prior methods and results in high-accuracy instance segmentation and counting despite the trees being tightly packed. Finally, we provide various forest image sequence datasets suitable for subsequent benchmarking and evaluation captured at different altitudes and leaf conditions.  more » « less
Award ID(s):
1835739
PAR ID:
10488422
Author(s) / Creator(s):
; ; ; ;
Publisher / Repository:
IEEE
Date Published:
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. We present a novel approach to perform instance segmentation and counting for densely packed self-similar trees using a top-view RGB image sequence. We propose a solution that leverages pixel content, shape, and self-occlusion. First, we perform an initial over-segmentation of the image sequence and aggregate structural characteristics into a contour graph with temporal information incorporated. Second, using a graph convolutional network and its inherent local messaging passing abilities, we merge adjacent tree crown patches into a final set of tree crowns. Per various studies and comparisons, our method is superior to all prior methods and results in high-accuracy instance segmentation and counting despite the trees being tightly packed. Finally, we provide various forest image sequence datasets suitable for subsequent benchmarking and evaluation captured at different altitudes and leaf conditions. 
    more » « less
  2. Tomaszewski, John E.; Ward, Aaron D. (Ed.)
    Automatic cell quantification in microscopy images can accelerate biomedical research. There has been significant progress in the 3D segmentation of neurons in fluorescence microscopy. However, it remains a challenge in bright-field microscopy due to the low Signal-to-Noise Ratio and signals from out-of-focus neurons. Automatic neuron counting in bright-field z-stacks is often performed on Extended Depth of Field images or on only one thick focal plane image. However, resolving overlapping cells that are located at different z-depths is a challenge. The overlap can be resolved by counting every neuron in its best focus z-plane because of their separation on the z-axis. Unbiased stereology is the state-of-the-art for total cell number estimation. The segmentation boundary for cells is required in order to incorporate the unbiased counting rule for stereology application. Hence, we perform counting via segmentation. We propose to achieve neuron segmentation in the optimal focal plane by posing the binary segmentation task as a multi-class multi-label task. Also, we propose to efficiently use a 2D U-Net for inter-image feature learning in a Multiple Input Multiple Output system that poses a binary segmentation task as a multi-class multi-label segmentation task. We demonstrate the accuracy and efficiency of the MIMO approach using a bright-field microscopy z-stack dataset locally prepared by an expert. The proposed MIMO approach is also validated on a dataset from the Cell Tracking Challenge achieving comparable results to a compared method equipped with memory units. Our z-stack dataset is available at 
    more » « less
  3. Convolutional neural networks trained using manually generated labels are commonly used for semantic or instance segmentation. In precision agriculture, automated flower detection methods use supervised models and post-processing techniques that may not perform consistently as the appearance of the flowers and the data acquisition conditions vary. We propose a self-supervised learning strategy to enhance the sensitivity of segmentation models to different flower species using automatically generated pseudo-labels. We employ a data augmentation and refinement approach to improve the accuracy of the model predictions. The augmented semantic predictions are then converted to panoptic pseudo-labels to iteratively train a multi-task model. The self-supervised model predictions can be refined with existing post-processing approaches to further improve their accuracy. An evaluation on a multi-species fruit tree flower dataset demonstrates that our method outperforms state-of-the-art models without computationally expensive post-processing steps, providing a new baseline for flower detection applications. 
    more » « less
  4. Liu, Weifeng (Ed.)
    Each year, numerous tornadoes occur in forested regions of the United States. Due to the substantial number of fallen trees and accessibility issues, many of these tornadoes remain poorly documented and evaluated. The process of documenting tree damage to assess tornado intensity is known as the treefall method, an established and reliable technique for estimating near-surface wind speed. Consequently, the demand for documenting fallen trees has increased in recent years. However, the treefall method proves to be extremely expensive and time-consuming, requiring a laborious assessment of each treefall instance. This research proposes a novel approach to evaluating treefall in large, forested regions using deep learning-based automated detection and advanced image processing techniques. The developed treefall method relies on high-resolution aerial imagery from a damaged forest and involves three main steps: (1) instance segmentation detection, (2) estimating tree taper and predicting fallen tree directions, and (3) obtaining subsampled treefall vector results indicating the predominant flow direction in geospatial coordinates. To demonstrate the method’s effectiveness, the algorithm was applied to a tornado track rated EF-4, which occurred on 10 December 2021, cutting through the Land Between the Lakes National Recreation Area in Kentucky. Upon observation of the predicted results, the model is demonstrated to accurately predict the predominant treefall angles. This deep-learning-based treefall algorithm has the potential to speed up data processing and facilitate the application of treefall methods in tornado evaluation. 
    more » « less
  5. 3D instance segmentation for unlabeled imaging modalities is a challenging but essential task as collecting expert annotation can be expensive and time-consuming. Existing works segment a new modality by either deploying pre-trained models optimized on diverse training data or sequentially conducting image translation and segmentation with two relatively independent networks. In this work, we propose a novel Cyclic Segmentation Generative Adversarial Network (CySGAN) that conducts image translation and instance segmentation simultaneously using a unified network with weight sharing. Since the image translation layer can be removed at inference time, our proposed model does not introduce additional computational cost upon a standard segmentation model. For optimizing CySGAN, besides the CycleGAN losses for image translation and supervised losses for the annotated source domain, we also utilize self-supervised and segmentation-based adversarial objectives to enhance the model performance by leveraging unlabeled target domain images. We benchmark our approach on the task of 3D neuronal nuclei segmentation with annotated electron microscopy (EM) images and unlabeled expansion microscopy (ExM) data. The proposed CySGAN outperforms pre-trained generalist models, feature-level domain adaptation models, and the baselines that conduct image translation and segmentation sequentially. Our implementation and the newly collected, densely annotated ExM zebrafish brain nuclei dataset, named NucExM, are publicly available at https://connectomics-bazaar.github.io/proj/CySGAN/index.html. 
    more » « less