Data_J_R_Soc_Interface_rsfi20150479

This zip file contains the raw data that have been used in Van Leeuwen JL, Voesenek CJ, Muller UK, J. R. Soc. Interface 12: 20150479 (http://dx.doi.org/10.1098/fsif.2015.0479). Three text files are provided on the data formatting (data_formats.txt), an overview of the swimming sequences (overview.txt), and the measured tail beat amplitudes for the swimming sequences (tail_amplitudes.txt). Raw video data (directory: Video), digitised longitudinal axis data (directory: Axes), and three-dimensional body models (directory: Body models) are arranged in three main directories

Inverse dynamics results of the simulated fish from Fig 3.

<p>The reference forces and torques were computed by applying our inverse dynamics method to the prescribed triangulated body shape. The grey lines correspond to the time points indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146682#pone.0146682.g003" target="_blank">Fig 3A</a>. (A) Resultant force on the fish, reference (thick, black) and tracked (thin, green) at a resolution of 1024 × 1024 pixels. (B) Resultant torque on the fish, reference (thick, black) and tracked (thin, green) at a resolution of 1024 × 1024 pixels. (C) Magnitude of the force error vector ||<b>F</b>_ref − <b>F</b>_calc|| and (D) the torque error vector for three resolutions of the generated images: 512 × 512 (light blue), 1024 × 1024 (medium blue) and 2048 × 2048 (dark blue) pixels, respectively approximately 170, 340 and 680 pixels along the fish. The grey bands indicate the first and last 5 frames that have reduced accuracy due to edge effects and may be cut off.</p

Overlap between the tracked fish and the video images of a three days post fertilisation zebrafish larva.

<p>The tracked fish (green) is overlayed over high-speed shadow images for a fast-start of a three days post fertilisation zebrafish larva, with its centre of mass indicated by white dots. Each row shows data from a different camera, from top to bottom oriented at: 30° to horizontal from the left, vertical, and 30° to horizontal from the right, as illustrated on the left hand side of each row. The first frame (0 ms) is shown in full, and zoomed in to the fish to illustrate the field of view size; the rest of the frames are only shown zoomed in.</p

Schematic overview of the tracking method.

<p>We provide initial information by creating a 3D model of the fish, calibrating the cameras and initialising the fish position by clicking the snout and tail position in the images from every camera (I). For every time step, we segment the fish in the images from all cameras and predict the fish position, orientation and body curvature based on previous frames (II). The predicted parameters are then used to initialise an optimisation algorithm. This algorithm finds the set of parameters (body curvature, position and orientation) that minimises the difference with the high-speed video frames (III). Once the optimisation has been performed for all frames, we compute the centre of mass and, by inverse dynamics, the resultant forces and torques over time (IV).</p

Errors in tracking of a simulated swimming fish, corresponding to the results shown in Fig 3.

<p>The grey lines correspond to the time points indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146682#pone.0146682.g003" target="_blank">Fig 3A</a>. (A) Magnitude of the error in snout (solid line) and centre of mass (dashed line) position, expressed by the Euclidean distance between the reference and tracked points. (B) Magnitude of the angle error vector of the head, expressed by the distance between the tips of the reference and the tracked rotation axis-angle representation. (C) Error in head–tail angle.</p

Post-processing result for a fast-start of a three days post fertilisation zebrafish larva.

<p>(A) Tracked fish model, time is shown by fill colour (from light grey to black), the path of the centre of mass is indicated by the orange line, with circles corresponding to each of the depicted fish shapes. The preparatory stroke is indicated by a narrow white line. The axes (<i>x</i>, <i>y</i>, <i>z</i>) define the world coordinate system, the axes (<i>x</i>_fish, <i>y</i>_fish, <i>z</i>_fish) define an instantaneous local coordinate system for the highlighted fish shape, defined in the deformation plane of the fish aligned with an inertia-weighted average of the local deformation angle. (B) Local body curvature (colours) along the fish length (horizontal) and time (vertical). The grays on the time axes correspond to the fish shapes in (A). (C) Resultant force on the body in “forward”, <i>x</i>_fish-, <i>y</i>_fish- and <i>z</i>_fish-direction, in respectively dark orange, light orange, light purple and dark purple. The “forward”, <i>x</i>_fish- and <i>y</i>_fish, <i>z</i>_fish-components are shown separately for reasons of clarity. (D) Resultant torque on the body in <i>x</i>_fish-, <i>y</i>_fish- and <i>z</i>_fish-direction, in respectively light orange, light purple and dark purple. The grayscale boxes on the time axes correspond to the fish shapes in each section in (E). (E) Time trace of the body shape in the world <i>x</i>, <i>y</i>- and <i>x</i>, <i>z</i>-plane (from light grey to black) for each of the 5 time-slices in (D) and (E), every second frame is shown.</p

Construction of the <i>in silico</i> zebrafish.

<p>(A) A series of cross-sectional shapes is combined into a three-dimensional body model. The cross-section indicated in blue is shown in more detail in (B). (B) Generation of cross-section in the tail region: two “components”, body (green) and fin (blue), with different cross-sectional shapes are merged into a single cross-section (black). (C) Parameterisation (position, head orientation and body curvature) of the three-dimensional body model. The position of the tip of the snout is described by the coordinates <i>x</i>, <i>y</i>, <i>z</i>, and head orientation by the three Tait-Bryan angles <i>φ</i>_roll, <i>φ</i>_pitch, <i>φ</i>_yaw. Body deformation is parameterised by prescribing a curvature <i>κ</i> along the centreline (red) at a number of control points, indicated by the dots; the body surface is deformed along with the centreline, under the assumption that the transverse sections stay plane, and perpendicular to the centreline.</p

Matlab datafile containing database

Matfile containing an array of structs with stimulus and response parameters for all measurement

examples of ovipositor insertions

This matlab file contains data on 3 different insertions in either 2% or 4% gel

animal spatial probing data and rheological data

This is a matlab file containing the rheological measurements of the used substrates (gels) as well as the data on spatial probing of all the wasps used in the study