7,657 research outputs found
SEGMENT3D: A Web-based Application for Collaborative Segmentation of 3D images used in the Shoot Apical Meristem
The quantitative analysis of 3D confocal microscopy images of the shoot
apical meristem helps understanding the growth process of some plants. Cell
segmentation in these images is crucial for computational plant analysis and
many automated methods have been proposed. However, variations in signal
intensity across the image mitigate the effectiveness of those approaches with
no easy way for user correction. We propose a web-based collaborative 3D image
segmentation application, SEGMENT3D, to leverage automatic segmentation
results. The image is divided into 3D tiles that can be either segmented
interactively from scratch or corrected from a pre-existing segmentation.
Individual segmentation results per tile are then automatically merged via
consensus analysis and then stitched to complete the segmentation for the
entire image stack. SEGMENT3D is a comprehensive application that can be
applied to other 3D imaging modalities and general objects. It also provides an
easy way to create supervised data to advance segmentation using machine
learning models
Automated detection of brain abnormalities in neonatal hypoxia ischemic injury from MR images.
We compared the efficacy of three automated brain injury detection methods, namely symmetry-integrated region growing (SIRG), hierarchical region splitting (HRS) and modified watershed segmentation (MWS) in human and animal magnetic resonance imaging (MRI) datasets for the detection of hypoxic ischemic injuries (HIIs). Diffusion weighted imaging (DWI, 1.5T) data from neonatal arterial ischemic stroke (AIS) patients, as well as T2-weighted imaging (T2WI, 11.7T, 4.7T) at seven different time-points (1, 4, 7, 10, 17, 24 and 31 days post HII) in rat-pup model of hypoxic ischemic injury were used to assess the temporal efficacy of our computational approaches. Sensitivity, specificity, and similarity were used as performance metrics based on manual ('gold standard') injury detection to quantify comparisons. When compared to the manual gold standard, automated injury location results from SIRG performed the best in 62% of the data, while 29% for HRS and 9% for MWS. Injury severity detection revealed that SIRG performed the best in 67% cases while 33% for HRS. Prior information is required by HRS and MWS, but not by SIRG. However, SIRG is sensitive to parameter-tuning, while HRS and MWS are not. Among these methods, SIRG performs the best in detecting lesion volumes; HRS is the most robust, while MWS lags behind in both respects
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