After installing Napari and Napari Animation, create a new Jupyter notebook file. To visualize images and create movies of the rendered zebrafish brain, load the 3D image and open the Napari window. Then connect the Napari animation plugin.
Next, set the parameters such as voxel size, color map, and contrast limits in the layer controls. Adjust the viewer settings in the canvas. Then to capture the rendered image, press the capture button in the animation wizard.
To generate movies of the rendered volume, modify the viewer settings and add key frames. After adding key frames, set the number of frames between key frames in the animation wizard. Finally, save the rendered animation.
The volumetric field of view of a larval zebrafish brain expressing pan neuronal GCaMP 7A covered the brain regions of the forebrain, midbrain, and hindbrain. Neuronal cell bodies of the medulla oblongata, cerebellar plate, optic tectum, hebenula, and dorsal telencephalon were clearly visible in the whole brain of a larval zebrafish. In 2D functional imaging, neuronal cell bodies were clearly visible in both the background and the superimposed neuronal activity.
