The Role of Biological Shape in Optical and Acoustic Measurements (thesis data)

The folder "MicroscopeImages" contains images of amphioxus tails where the animal is denoted by the letter in the file name and the time point (days post-amputation) is denoted by the number in the file name.

The folder "OCTimages" contains all OCT images arranged into folders where the letter in the folder title denotes the animal and the number denotes the time point (days post-amputation). There are three additional folders: x containing images of a B. lanceolatum tail; y containing images of a B. floridae tail; Head containing images of a B. lanceolatum head. Within each folder are OCT images, in JPEG or PNG format, are numbered sequentially.

The file "tpsfile_AmphioxusLandmarks" contains the digitised landmark from the OCT images of amphioxus and a series of simple shapes. This file can be read as a text file or used with the open source TPS series of software. The file "LandmarkIndex.csv" contains an index of the landmarks contained within the file "tpsfile_AmphioxusLandmarks". The orders within both files are identical.

The folder "ShapeProfiles" contains 147 krill shape profiles compatible with ZooScatR. Each shape profile represents a realistic krill shape. An additional generic shape profile, "AvShape", is included, which is the average of the other 147 krill shapes.

The folder "Simulations" contains the following files:
*"AcousticSimulations.csv" - 999 simulations of krill acoustic density (m^2 nmi^-2)
*"Biomass_GenericShape.csv" - 999 simulations of krill biomass (mtons) and density (gm^-2) produced with the generic shape
*"Biomass_ShapeCatalogue.csv" - 999 simulations of krill biomass (mtons) and density (gm^-2) produced with the shape catalogue
*"ConversionFactor_GenericShape.csv" - 999 simulations of the conversion factor (g nmi^2 m^-4) produced with the generic shape
*"ConversionFactor_ShapeCatalogue.csv" - 999 simulations of the conversion factor (g nmi^2 m^-4) produced with the shape catalogue
*"ShapeSimulations.csv" - 999 simulations of lists of shapes
*"SurveyBoundary.csv" - a survey boundary
*"TargetStrength_GenericShape_120kHz.csv" - krill target strength to length relationship for the generic shape at 120kHz over a range of in situ orientation distributions
*"TargetStrength_ShapeCatalogue_120kHz.csv" - 999 simulations of krill target strength to length relationship for the shape catalogue at 120kHz over a range of in situ orientation distributions
"WetMassSimulations.csv" - 999 simulations of the wetmass to length relationship for krill