3D reconstructions of semi-transparent submerged objects: Nanomia, Cystisoma, and validation object

These data were used to support the conclusions published in the article titled, "New method for rapid 3D reconstruction of semi-transparent underwater animals and structures", accepted for publication in Integrative Organismal Biology on May 9th, 2023.

It focuses on three physical objects, two of which were live animals, collected under permit in the Monterey Bay NAtional MArine Sanctuary:

A siphonophore of the species Nanomia bijuga

An amphipod of the family Cystisoma

A thin-walled plastic cylinder, for validation purposes.

For each of these objects, we provide the original .cine file, as recorded by the Phantom 640S highspeed camera, and the derived high-quality .mov video file. We exported video frames as image stacks, included as ZIP files in this repository. We chose to either extract the red or green channel, or a balanced luminance value of each frame. Background subtraction was performed in some cases, by applying a minimum filter or median filter with a certain Z (time axis) extent, and subtracting this from the original frames. Furthermore, additional smoothing was performed in some cases as indicated by the filenames, in the form of a median filter with an X-by-Y-by-Z extent.

3D Slicer software was used for segmentation, and bundled .mrb files are included, which have been tested with 3D Slicer version 5.0.3. Derived .STL or .PLY model files are included as well.