DOI: 10.5061/dryad.7d7wm3829
title: Data from: The effect of external flow on 3D orientation of a microscopic sessile suspension feeder, Vorticella convallaria

description: Vorticella convallaria are microscopic sessile suspension feeders that
 live attached to substrates in aquatic environments. They feed using a
 self‐generated current and help maintain the health of aquatic ecosystems
 and wastewater treatment facilities by consuming bacteria and detritus.
 Their environmental impact is mediated by their feeding rate. In ambient
 flow, feeding rates are highly dependent on an individual's
 orientation relative to the substrate and the flow. Here, we investigate
 how this orientation is impacted by flow speed. Furthermore, we examined
 whether individuals actively avoid orientations unfavorable for feeding.
 We exposed individuals to unidirectional laminar flow at shear rates of 0,
 0.5, 1.0, and 1.5 s−1, and recorded their 3D orientation using a custom
 biplanar microscope. We determined that V. convallaria orientation became
 progressively tilted downstream as the shear rate increased, but
 individuals were still able to actively reorient. Additionally, at higher
 shear rates, individuals spent a larger fraction of their time in
 orientations with reduced feeding rates. Our shear rates correspond to
 freestream flows on the scale of mm s−1 to cm s−1 in natural environments.
description: Please see details in the methods section of  T. Böttger, B.
 Klaassen van Oorschot, and R. E. Pepper, “The effect of external flow on
 3D orientation of a microscopic sessile suspension feeder, Vorticella
 convallaria,” <em>Annals of the New York Academy of
 Sciences</em>, doi: 10.1111/nyas.15170.
description: # **Data and code from The effect of external flow on 3D orientation of a
 microscopic sessile suspension feeder, Vorticella convallaria**  These
 data consist of: 1\)     Matlab data files (.mat), which are raw data of
 angle vs. time for the cell body and stalk of 15 individuals. Details of
 the data files are described below. 2\)   
 plot_vorticella_angle_data.ipynb is a Python notebook that illustrates how
 to use the Matlab data files in Python if desired. 3\)    R code to do the
 statistical analyses described in our paper. This code contains further
 comments with details of each analysis. 4\)    Vorticella_data.xlsx. An
 Excel file that contains all data used in the R code in a format suitable
 for use with this code. Details of this data file are described below. 
 5\)    Flow channel laser cutter outlines.cdr and Flow channel laser
 cutter outlines.pdf. These files are to-scale outlines of the laser cut
 pieces used to make the flow chamber used in our experiments. The cored
 draw (.cdr) file can be used directly with many laser cutter to cut the
 needed shapes. # Description of Matlab raw data: The file name gives the
 vorticella individual identifier and the flow shear rate in inverse
 seconds as “vort###shear###.mat” These Matlab files contain the following
 variables: * t: the time in seconds * bphi: The body phi angle in degrees
 (azimuthal angle). * btheta: The body phi angle (polar angle). * sphi: The
 stalk phi angle in degrees (azimuthal angle). * stheta: The stalk theta
 angle (polar angle). The format of the data is such that plot(t,bphi) will
 make a vector plot of the body phi as a function of time. The
 plot_piv_data.ipynb notebook will also import the Matlab data files and
 plot a vector plot of the velocity fields. # Description of Excel data:
 This Excel file has the following labeled columns: * indiv_num: A number
 that identifies each individual organism. These numbers match the numbers
 referenced in Böttger et al. * vort_num: A number that identifies each
 individual organism. These numbers match the matlab file names. * shear:
 The shear rate that the organism was exposed to * order: The order of
 exposure (i.e 1 means exposed to this shear rate first). * time_min: The
 time point of this data (in minute) * bodyphi: The phi angle of the cell
 body * bodytheta: The theta angle of the cell body * stalkphi: The phi
 angle of the stalk * stalktheta: The theta angle of the stalk *
 peristome_height_mm: The height of the peristome above the surface in mm.
 * stalk_length_mm: The length of the stalk in mm * peristome_dia_avg_mm:
 The diameter of the peristome in mm averaged over several measurements for
 each individual. * frscaled: The scaled feeding rate for each organism at
 each time point. These are scaled by the feeding rate_vert column and this
 scaling is described further in Böttger et al.  Data were filtered to
 remove outliers which represent times when Vorticella were contracting. At
 these time points this column contains no data. The Excel file is
 optimized to work with the R code. Modifying the empty cells may disrupt
 the code intended for file analysis. * frscaledmean: The mean value of the
 scaled feeding rate (previous column) for each individual at each shear
 rate. * inrecirc: Whether the organism is predicted to be at an
 orientation that leads to recirculation in the flow through the organisms
 feeding rate. The value 0 means not predicted to be in an orientation with
 recirculation at that time, 1 means predicted to be in an orientation with
 recirculation at that time.  * fracinrecirc: The fraction of time this
 individual at that flow speed spends in orientations predicted to lead to
 recirculation. * feedingrate_vert: The predicted feeding rate for this
 individual at this flow speed when oriented vertically in m^3/s. #
 Description of individual identifier number: Both the matlab and excel
 data use identifier number for individual organisms. These match between
 the matlab and excel and correspond to the individuals referenced in
 Böttger et al as follows: Individual 1: 020 Individual 2: 013 Individual
 3: 015 Individual 4: 007 Individual 5: 009 Individual 6: 010 Individual 7:
 017 Individual 8: 018 Individual 9: 021 Individual 10: 022 Individual 11:
 024 Individual 12: 025 Individual 13: 027 Individual 14: 032 Individual
 15: 033