Automated processing of zebrafish imaging data:
List of zebrafish-specific and general tools, application- and method-oriented papers
This Excel table is an additional material to the accepted survey paper:
R. Mikut, T. Dickmeis, W. Driever, P. Geurts, F. Hamprecht, B. X. Kausler, M. J. Ledesma-Carbayo, R. Marée, K. Mikula, P. Pantazis, O. Ronneberger, A. Santos, R. Stotzka, U. Strähle, N. Peyriéras.
Automated processing of zebrafish imaging data - a survey. Zebrafish. 2013, 10, 401-421
Please refer to this paper if you use this Excel table.
Please help the authors to improve this Excel table.
Contact: ralf.mikut@kit.edu
Three parts in different tables:
* Zebrafish-specific tools:
Inclusion criteria:
Image processing software tools or integrated systems with a focus on zebrafish (available or at least announced)
* Relevant general tools:
Inclusion criteria:
Image processing software tools or integrated systems with a general focus,
but potentially useful for zebrafish image processing.
The more specific tools should have at least one successful applications to zebrafish.
* Application and method oriented papers:
Inclusion criteria:
Original method or application papers with automated image processing methods with a focus to zebrafish (no surveys).
Subfolder Contents:
SpinalCordMethods Extension Package:
* Contains a set of functions and Gait-CAD plugins for the automated information extraction of neuronal patterns in the spinal cord of zebrafish.
* Corresponding publication: J. Stegmaier, M. Shahid, M. Takamiya, L. Yang, S. Rastegar, M. Reischl, U. Strähle, R. Mikut. (2013) Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish. Bioinformatics. 2014 (30), 726-733
http:/dx.doi.org/10.1093/bioinformatics/btt600
Heartbeat:
This software implements an in-vivo method for fully automatic detection and analysis of heartbeats in videos of non-fixed and non-anaesthetized zebrafish embryos. This software is supplementary material to the paper
Christian Pylatiuk, Daniela Sanchez, Ralf Mikut, Rüdiger Alshut, Markus Reischl, Sofia Hirth, Steffen Just, Wolfgang Rottbauer:
Automatic Zebrafish Heartbeat Detection and Analysis. Zebrafish. 2014 (11), 379-383
