summarize reflectance and shape according to wing grids Begin with 'generate_group_list_v2.nb' which converts the group table from csv format to json format. An alternative way is manually preparing a json file. Once we have the group json file, we open 'specimen_group_summary.m' and specify the parameters before execute it.
Please find the article describing the application of this script below (DOI: 10.1038/s42003-022-04282-z): (https://www.nature.com/articles/s42003-022-04282-z)
Exemplar datasets can be found in this repository: (https://doi.org/10.5061/dryad.37pvmcvp5)
Please find the link for the corresponding protocol: (https://www.protocols.io/private/F3292DF1FE0211EB878B0A58A9FEAC02)
Please cite this work as: Chan, W-P., Rabideau Childers, R., Ashe, S. et al. A high-throughput multispectral imaging system for museum specimens. Commun Biol 5, 1318 (2022).
%{1}= average reflectance
%{1}{1} = dorsal side
%{1}{2} = ventral side
%{1}{}{1}=forewing
%{1}{}{2}= hindwing
%{}{}{}{n}=the mean reflectance of bandID (the order is the same as the matrix read in)
%{2}= standard deviation of reflectance (inter species)
%{2}{1}= standard deviation of reflectance (inter species) at dorsal side (high value indicates regions different from different individual)
%{2}{2}= standard deviation of reflectance (inter species) at ventral side (high value indicates regions different from different individual)
%{2}{3}= average spatial standard error of reflectance (inter species) at dorsal side (high value indicates high contrast region)
%{2}{4}= average spatial standard error of reflectance (inter species) at ventral side (high value indicates high contrast region)
%{2}{}{1}=forewing
%{2}{}{2}= hindwing
%{2}{}{}{n}=the reflectance of bandID (the order is the same as the matrix read in)
%{3}= mean shape
%{}{1}=overall mean shape of forewing
%{}{2}=overall mean shape of hindwing
%{}{}{1}=mean shpe mask
%{}{}{2}=mean shpe regPts
%{}{}{3}=mean shpe grids
%{}{3}=mean shape of forewing of each specimen
%{}{4}=mean shape of hindwing of each specimen
%{4}= specimen level tail summary data
%{4}{N}= No.N specimen
%{4}{}{1}=specimen barcode
%{4}{}{2}=with tail or not (1, 0)
%{4}{}{3}= the probability of having a tail in a postion under the condition that the specimen does have a tail
%(x=1: First column in the grid; x=2: Last row in the grid; y: concessive grids; z: probability)
%{4}{}{4}= the mean length of those tails at each position
%(x=1: First column in the grid; x=2: Last row in the grid; y: concessive grids; z: tail length)
%{4}{}{5}= the mean curvature of those tails at each position
%(x=1: First column in the grid; x=2: Last row in the grid; y: concessive grids; z: tail curvature)
%{4}{}{6}= the range of length of those tails at each position %See {4}{4}
%{4}{}{7}= the range of curvature of those tails at each position %See {4}{5}
%{4}{}{8}= a matrix which integrated tail length data for both left and right hindwings
%(x=1: First column in the grid; x=2: Last row in the grid; y: concessive grids; z: left or right wing)
%{4}{}{8}(:,:,1) = left hindwing
%{4}{}{8}(:,:,2) = right hindwing
%{5}= tail summary information (not normally distributed so use median and IQR)
%{5}{1} = the probability of having a tail in a postion under the condition that the specimen does have a tail
%(x=1: First column in the grid; x=2: Last row in the grid; y: concessive grids; z: probability)
%{5}{2} = the median length of those tails at each position
%(x=1: First column in the grid; x=2: Last row in the grid; y: concessive grids; z: tail length)
%{5}{3} = the median curvature of those tails at each position
%(x=1: First column in the grid; x=2: Last row in the grid; y: concessive grids; z: tail curvature)
%{5}{4} = the IQR of length of those tails at each position %See {5}{2}
%{5}{5} = the IQR of curvature of those tails at each position %See {5}{3}
%{5}{6} = a 3d matrix which integrated all original tail length data
%(x=1: First column in the grid; x=2: Last row in the grid; y: concessive grids; z: tails but not specimens)
%{6}= antenna summary information
%{6}{1} = multispectral reflectance of dorsal side of antennae
%{6}{2} = multispectral reflectance of ventral side of antennae
%{6}{1 | 2}{1} = mean
%{6}{1 | 2}{1} = standard deviation
%{6}{1 | 2}{}(:,1) = 740
%{6}{1 | 2}{}(:,2) = 940
%{6}{1 | 2}{}(:,3) = UV
%{6}{1 | 2}{}(:,4) = UVF
%{6}{1 | 2}{}(:,5) = F
%{6}{1 | 2}{}(:,6:8) = white (RGB)
%{6}{1 | 2}{}(:,9:11) = whitePo1 (RGB)
%{6}{1 | 2}{}(:,12:14) = whitePo2 (RGB)
%{6}{1 | 2}{}(:,15:17) = FinRGB (RGB)
%{6}{1 | 2}{}(:,18:20) = PolDiff (RGB)
%{6}{3} = antennae morphology measurements (normal distributed so use mean and sd)
%{6}{3}{1} = mean
%{6}{3}{2} = standard deviation
%{6}{3}{}(1) = Antennae length (mm)
%{6}{3}{}(2) = Antennae width (mm)
%{6}{3}{}(3) = Bulb width (mm)
%{6}{3}{}(4) = Curviness (unitless)
%{6}{4} = filter indicating those dorsal-side antennae being included in the analysis; 0: excluded; 1: included
%{6}{5} = filter indicating those dorsal-side antennae being included in the analysis; 0: excluded; 1: included
%{7} = scale length
%{7}{1} = dorsal
%{7}{2} = ventral
%{8} = The list of original file information