Computational protocol: Ethanol Affects the Development of Sensory Hair Cells in Larval Zebrafish (Danio rerio)

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Protocol publication

[…] All specimens were whole mounted in either Vectashield (Vector Labs, Burlingame, CA) or glycerol/PBS (9:1). Images of lateral line neuromasts were obtained using a Leica TCS SP confocal laser-scanning microscope (Leica Microsystems, Heidelberg, Germany) or a Nikon-C1-SI confocal microscope (Nikon Instruments Inc., Melville, NY). Single images and compressed z-series were collected with Leica Software (Leica Microsystems) or EZ-C1 software (Nikon Instruments). Cell counts were performed at the time of imaging by viewing the image slices sequentially. Alternatively, images were obtained using a Nikon Eclipse Ni Fluorescence Microscope (Nikon Instruments) using a 60X objective and video images were obtained using a Nikon DS-Qi1 Cooled CCD camera and NIS Elements software (Nikon Instruments). Both the O2 and Mi1 neuromasts were imaged for all of the experiments. These neuromasts were studied since they are easily identifiable and have been used in previous studies , . The entire neuromast can be observed in one field of view when the larval zebrafish is mounted on its side. Images were scaled and cropped using Adobe Photoshop (Adobe Systems, San Jose, CA), ImageJ (National Institutes of Health, Bethesda, MD), or Nikon EZ-C1 software. [...] Statistical analyses were performed using either an unpaired two-sample t-test assuming unequal variances (Excel; Microsoft Corporation, Redmond, WA), a one-way analysis of variance (ANOVA; Statistica, StatSoft Inc., Tulsa, OK), or VassarStats (Vassar College, Poughkeepsie, NY). Post-hoc comparisons, when appropriate, utilized the Tukey-Kramer HSD test. Alternatively, the data were analyzed using analysis of covariance (ANCOVA) using SPSS (IBM Corporation, Armonk, NY). […]

Pipeline specifications

Software tools ImageJ, Statistica, VassarStats, SPSS
Applications Miscellaneous, Laser scanning microscopy, Microscopic phenotype analysis
Organisms Danio rerio, Homo sapiens
Diseases Nervous System Malformations, Fetal Alcohol Spectrum Disorders
Chemicals Ethanol, Methanol, Bromodeoxyuridine