#43454 SHAPER PDF FULL#

To get the calibration measurements, use an image manipulation program and measure 1mm on the calibration measurement stick and register how many pixels 1mm is into the column 'cal'. Summary statistics of each otolith (otolith area, length, perimeter and width) can be obtained if the calibration measurements in pixels have been registered in the csv data file in a column labelled 'cal' (see example data file).

If other measurements are used (fish weight, otolith weight etc.) a column for each parameter needs to be given in the data file. The column 'length_cm' needs to exist so it is possible to remove the allometric growth effect on otolith shape. '403_1'), which are used to link biological information for each fish to the otolith outline. Two columns in the data file are mandatory, 'folder' (consists of folder names such as 'IC') and 'picname' (consists of file names e.g. (see data file example) is stored in the 'ShapeAnalysis' folder as a text file in a csv format (*.csv).

An otolith image name in folder 'IC' should be in the format '403_1', '403_2', '403_3', etc where the first three letters represent the station number and the second number, after the underscore, represents the fish number.Ī data file for each fish specimen (in rows), with information in columns such as population, station nr, sampling date, location, length, maturity stage, etc. For example, 'IC' would represent a sample from Iceland. The area-folders in the folders 'Original' and 'Fixed' should be named with two letters of the sampling unit, or country, and the station number of the sample. The folders 'Original' and 'Fixed' need to exist because images in both folders are used when the shapeR package is used to perform quality checks on the otolith outlines. For the ease of handling the images, make a folder called 'ShapeAnalysis' and store the images from each sampling unit in a unique area-folder within a folder called 'Original', and make a copy of the whole folder 'Original' and name it 'Fixed'. The otoliths need to be orientated with their rostrum to the left as seen in Fig.

#43454 SHAPER PDF FULL#

Images should then be taken and stored in full color, ensuring good focus and high resolution in jpeg format (*.jpg). When the settings are ready, an image of a calibration measurement stick, in good focus, is taken as a size reference. The microscope should be tuned so an otolith on a black background is as clear as possible. 1) using a dissection microscope with a digital camera attached. The first step of the shape analysis is to capture the otolith images ( Fig.

While the Fourier transform provides functions in the form of sines and cosines which are non-local and can therefore result in poor approximations of sharp edges, the Wavelet transform uses approximating functions that are contained in finite domains making them well-suited for approximating sharp edges. The Wavelet transform provides a powerful alternative to the more commonly applied Fourier transform in shape analysis.

There are built-in functions which allow users to perform automatic processes such as extract the otolith outlines from images, visualize the mean shape, smooth the outline by eliminating pixel noise and transform the outlines into independent coefficients using either Normalized Elliptic Fourier or Discrete Wavelet, which can be entered into a wide range of statistical packages in R. Here, we present an R package to extract, visualize and generate otolith shape data with a small number of easy-to-use functions. The advantage of using such methods in population identification is that they are cost effective and only require otolith images from which outlines can be extracted and analysed with statistical software. With outline analysis it is possible to quantify boundary shapes so that patterns of shape variation within and among groups can be evaluated based on a large number of independent variables. For otolith shape analysis, two main morphometric methods are used: landmark analysis and outline analysis. Morphometric analysis of otoliths is a well-established method to delineate fish stocks, characterize population movements and to detect the natal origin of fish.

43454 shaper pdf