Welcome to the online repository for the Zebrafish Visual Motor Response (VMR) Analytical Tool. This tool is designed for re-coding (the output raw activity data file) and analyzing VMR data collected from zebrafish larvae using ZebraLab by ViewPoint. Building a VMR analytical pipeline is an ongoing effort, hence all codes in this repository may undergo changes to accommodate different research projects and publications. Our development of the analytical pipeline is informed by the pioneering work of researchers in the VMR assay field. Please see the references section at the end of this document for further details.

The following publications have utilized this pipeline for their research, demonstrating its application and utility in the field:

1. A zebrafish model system for studying the ANGPT/TIE2 pathway and glaucoma.
   Shi Song Rong; Anna Larson; Janey L Wiggs.
   Investigative Ophthalmology & Visual Science June 2022, Vol.63, 1130.

2. A hidden structural variation in a known IRD gene: a cautionary tale of two new disease candidate genes.
   Scott HA, Larson A, Rong SS, Mehrotra S, Butcher R, Chao KR, Wiggs JL, Place EM, Pierce EA, Bujakowska KM.
   Cold Spring Harb Mol Case Stud. 2022 Mar 24;8(2):a006131.
   DOI: 10.1101/mcs.a006131. PMID: 34728537

3. Rare ATXN2 Variants in Cases with Primary Open Angle Glaucoma Cause Visual Impairment in Zebrafish.
   Shi Song Rong; Anna Larson; John Simmons Borchert; Janey L Wiggs.
   Investigative Ophthalmology & Visual Science July 2019, Vol.60, 2833.

4. Functional annotation of glaucoma-associated ATXN2 variants using zebrafish.
   Shi Song Rong; Louis R. Pasquale; Anna Larson; Kinga Maria Bujakowska; Janey L Wiggs.
   Investigative Ophthalmology & Visual Science July 2018, Vol.59, 5157.

To further explore the background and methodology behind the VMR assay, please consult the following key references:

1. Emran, F., Rihel, J. & Dowling, J. E. A behavioral assay to measure responsiveness of zebrafish to changes in light intensities. J Vis Exp, DOI:10.3791/923 (2008).

2. Liu, Y. et al. Statistical Analysis of Zebrafish Locomotor Response. PLoS One 10, e0139521, DOI:10.1371/journal.pone.0139521 (2015).

For further information or inquiries, please contact:

Shi Song Rong @ Massachusetts Eye and Ear, Harvard Medical School, Mass General Brigham, Boston