Segmentation and quantification of fertilization calcium dynamics in Caenorhabditis elegans

---

Brief information about this project:

• We developed ImageJ plugins to segment oocyte region labeled with a calcium indicator dye in a time lapse image stack.

Publication:

• Takayama, J., Fujita, M., and Onami, S. (2017). In vivo live imaging of calcium waves and other cellular processes during fertilization in Caenorhabditis elegans. Bio Protoc. 7, e2205. doi: 10.21769/BioProtoc.2205. [OpenAccess]
• Takayama, J. and Onami, S. (2016). The sperm TRP-3 channel mediates the onset of a Ca²⁺ wave in the fertilized C. elegans oocyte. Cell Rep. 15, 625-637. [PubMed][Open Access]

Software:

• Requirements
  
• ImageJ 1.49v or later.
  
• Download
• Calculator_Plus3.java [ source code (9 kB)] [ Calculator_Plus3.class (6 kB)]
• ContourTrack3Stack_.java [ source code (8 kB)] [ ContourTrack3Stack_.class (3 kB)]
• ContourTrack4Stack_.java [ source code (8 kB)] [ ContourTrack4Stack_.class (3 kB)]
• Layer_Test2M.java [ source code (7 kB)] [ Layer_Test2M.class (5 kB)] [ Layer_Test2M$LayeredImageM.class (3 kB)]
• TrackOocyte_.java [ source code (10 kB)] [ TrackOocyte_.class (4 kB)] [ LabelHolder.class (1 kB)]
• RoughQuantify_.java [ source code (3 kB)] [ RoughQuantify_.class (3 kB)]
• all plugins (zip) [ source code (20 kB)] [ class (21 kB)]

Please contact us if you have any problems or questions.

Shuichi Onami
Laboratory for Developmental Dynamics
RIKEN Quantitative Biology Center
2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047 Japan
URL: http://so.qbic.riken.jp
E-mail: sonami@riken.jp