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Spatial drift correction of zebrafish images

KK Keiichi Katsumoto
SY Siham Yennek
CC Chunguang Chen
LS Luis Fernando Delgadillo Silva
ST Sofia Traikov
DS Dror Sever
AA Ajuna Azad
JS Jingdong Shan
SV Seppo Vainio
NN Nikolay Ninov
SS Stephan Speier
AG Anne Grapin-Botton
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The red channel (cdt1-mCherry) signal from the β-cell nuclei was used to correct for spatial drift in the green GCaMP6s channel. We employed the Fiji plugin ‘Descriptor-based series registration (2d/3d + t)’ (https://imagej.net/Descriptor-based_registration (2d/3d))55, applying the model ‘Rigid (2d)’, with ‘3-dimensional quadratic fit’. A σ of 13 and threshold of 0.03 were applied to the detection of nuclear signal, with a minimum number of three neighbors, redundancy of 1 and a random sample consensus (Ransac) error of 5. Matching across time series was achieved using global optimization.

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