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Automatic tracking of multiple cell regions in 4D live-cell imaging data

Research Project

Project/Area Number 15K16021
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Perceptual information processing
Research InstitutionKanazawa University

Principal Investigator

Hirose Osamu  金沢大学, 電子情報学系, 助教 (30549671)

Research Collaborator Kawaguchi Shotaro  金沢大学
Tokunaga Terumasa  九州工業大学
Yoshida Ryo  統計数理研究所
Toyoshima Yu  東京大学
Teramoto Takayuki  九州大学
Kuge Sayuri  九州大学
Ishihara Takeshi  九州大学
Iino Yuichi  東京大学
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords物体追跡 / 粒子フィルタ / マルコフ確率場 / ベイズ推定 / 人工知能 / 機械学習 / 4Dライブセルイメージングデータ / ライブセルイメージングデータ / 時系列解析
Outline of Final Research Achievements

In this research, we aimed at developing the methods for automating the detection and tracking of cell regions in 4D live-cell imaging data. Cells in 4D live-cell imaging data are often imaged as ellipsoidal shapes and are densely distributed. For this data, standard methods usually fail to automatic tracking because of cell-switching and coalescence of tracked positions. To address this issue, we utilized typical characteristics in 4D live-cell imaging data; movements of nearly-located cells are strongly correlated. By using the characteristics used as the information for predicting cells' positions, we succeeded to improve tracking performance drastically. The software developed in this research is being distributed on the project website.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (8 results)

All 2017 2016 2015 Other

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 2 results) Presentation (4 results) (of which Int'l Joint Research: 2 results) Remarks (2 results)

  • [Journal Article] SPF-CellTracker: Tracking multiple cells with strongly-correlated moves using a spatial particle filter2017

    • Author(s)
      Hirose Osamu、Kawaguchi Shotaro、Tokunaga Terumasa、Toyoshima Yu、Teramoto Takayuki、Kuge Sayuri、Ishihara Takeshi、Iino Yuichi、Yoshida Ryo
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: - Issue: 6 Pages: 1-1

    • DOI

      10.1109/tcbb.2017.2782255

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space.2016

    • Author(s)
      Toyoshima Y, Tokunaga T, Hirose O, Kanamori M, Teramoto T, Jang MS, Kuge S, Ishihara T, Yoshida R, Iino Y.
    • Journal Title

      PLoS Comput Biol.

      Volume: 12 Issue: 6 Pages: 1-20

    • DOI

      10.1371/journal.pcbi.1004970

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] SPF-CellTracker: Multiple cell tracking with strongly-correlated moves using spatial particle filter2015

    • Author(s)
      Osamu Hirose
    • Organizer
      Bioimage Informatics 2016
    • Place of Presentation
      National Institute of Standards and Technology, Washington DC
    • Year and Date
      2015-10-13
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] SPF-CellTracker: Multiple cell tracking with strongly-correlated moves using spatial particle filter2015

    • Author(s)
      Osamu Hirose
    • Organizer
      GIW/InCoB 2016
    • Place of Presentation
      Kagaku-Miraikan, Odaiba, Tokyo
    • Year and Date
      2015-09-01
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] 空間粒子フィルタによる多数の細胞の同時追跡2015

    • Author(s)
      広瀬 修
    • Organizer
      第21回IBISML研究会 - 情報論的学習理論と機械学習 (IBISML)
    • Place of Presentation
      沖縄研,沖縄科学技術大学院大学
    • Year and Date
      2015-06-23
    • Related Report
      2015 Research-status Report
  • [Presentation] 空間粒子フィルタによる多数の細胞の同時追跡2015

    • Author(s)
      広瀬 修
    • Organizer
      バイオイメージ・インフォマティクス ワークショップ 2015
    • Place of Presentation
      福岡県,九州大学
    • Year and Date
      2015-06-18
    • Related Report
      2015 Research-status Report
  • [Remarks] SPF-CellTracker

    • URL

      https://github.com/ohirose/spf

    • Related Report
      2017 Annual Research Report 2016 Research-status Report
  • [Remarks] https://github.com/ohirose/spf

    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2019-03-29  

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