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Abstract
Results: We developed a new method, termed as DELICATE, that dramatically improves the accuracy of automated cell lineage tracing especially during the stage post 350 cells of C. elegans embryo. DELICATE works by increasing the local SNR and improving the evenness of nuclei fluorescence intensity across cells especially in the late embryos. The method both dramatically reduces the segmentation errors by StarryNite and the time required for manually correcting tracing errors up to 550-cell stage, allowing the generation of accurate cell lineage at large-scale with a user-friendly software/interface.
Availability and implementation: All images and data are available at https://doi.org/10.6084/m9.figshare.26778475.v1. The code and user-friendly software are available at https://github.com/plcx/NucApp-develop
© The Author(s) 2024. Published by Oxford University Press.
Original language | English |
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Article number | btae626 |
Number of pages | 8 |
Journal | Bioinformatics |
Volume | 40 |
Issue number | 11 |
Online published | 17 Oct 2024 |
DOIs | |
Publication status | Published - Nov 2024 |
Funding
This work was supported by the General Research Funds (HKBU12101520, HKBU12101522, HKBU12101323) from the Hong Kong Research Grants Council, Hong Kong Innovation and Technology Fund (GHP/176/21SZ), and Initiation Grant for Faculty Niche Research Areas (RC-FNRA-IG/21–22/SCI/02) from Hong Kong Baptist University to Zhongying Zhao, and Hong Kong Innovation and Technology Commission (InnoHK Project CIMDA), Hong Kong Research Grants Council (11204821), and City University of Hong Kong (project 9610034) to Hong Yan.
Research Keywords
- Deep Learning
- C. elegans
- Image-enhancement
- Lineage-tracing
- Fluorescence
Publisher's Copyright Statement
- This full text is made available under CC-BY 4.0. https://creativecommons.org/licenses/by/4.0/
Fingerprint
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GRF: Matching Large Feature Sets based on Hypergraph Models and Structurally Adaptive CUR Decompositions of Compatibility Tensors
YAN, H. (Principal Investigator / Project Coordinator)
1/01/22 → …
Project: Research