Veith_et_al_2024/microCT/README.md

Micro CT data

PMA (phosphomolybdic acid)-stained, adult, male Danionella cerebrum.

See https://danionella.github.io/veith_et_al_2024/ for online viewer.

See http://n2t.net/ark:/87602/m4/623999 for MorphoSource entry.

Raw data

Danionella_cerebrum_PMA_16bit_binned_1p297_oriented_front_1965x1926x3328.raw
When opening file in ImageJ Fiji, choose 16-bit Unsigned and Little-endian byte order. Opening as virtual stack is recommended. The voxel size is 1.29702 µm.

Segmentation (DragonFly)

Danionella_cerebrum_PMA_16bit_binned_1p297_oriented_front_1965x1926x3328_cropped_1224x1224x1645_segmentation.ORSSession
Dragonfly (https://www.theobjects.com/dragonfly) project file, which contains raw data cropped around the inner ear (1224x1224x1645, anchor at 369,246,412), handlabelled planes, interpolated binary ROIs (interpolated by biomedisa, https://biomedisa.info/), and meshgrids derived from these binary ROIs.

Meshgrids (Blender)

Danionella_cerebrum_PMA_16bit_binned_1p297_oriented_front_1965x1926x3328_cropped_1224x1224x1645_meshgrid.blend
This Blender project file contains downsampled meshgrids of segmented inner ear structures and an animation.