keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/main_disp_spline.m | .m | 818 | 31 | %Spline n = 3
t = -3:0.01:3;
x = t;
x = abs(x);
ind0 = (x >= 0 & x < 1);
ind1 = (x >= 1 & x < 2);
ind2 = (x >= 2);
x(ind0) = 2/3 - x(ind0).^2 + x(ind0).^3/2;
x(ind1) = (2 - x(ind1)).^3/6;
x(ind2) = 0;
figure,plot(t,x);hold on;
fprintf('Integral of Spline basis %1.2e\n',sum(x)*0.01);
x = t;
x = abs(x);
%F^{-1} of sinc^... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/saveResults_old.m | .m | 10,248 | 203 | function saveResults_old(results, results_mol, results_graph,res_folder)
%SAVERESULTS_OLD Save all the results
%Save results in final file
fname = ['results____',...
results{1}.participant,'.csv'];
fileID = fopen(strcat(res_folder,filesep,...
results{1}.participant,filesep,fname),'w');
formatSpec = strcat('%s,... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/im_metrics.m | .m | 4,365 | 134 | function [Iref,Iest,varargout] = im_metrics(posEst,posRef,sig,pix_size,im_size,winLen,areaCenter,doFSC,varargin)
%im_metrics Provides image based metrics : SNR, FRC
% image obtained by convolving the positions with a gaussian (sigma sig)
% SNR = 10*log_10(norm(posRef_gauss,2)^2/norm(posRef_gauss-posEst_gauss,2)^2)
... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/assessment_mol.m | .m | 2,642 | 73 | function perf_metrics = assessment_mol(fpath, result_fname)
%ASSESSMENT_MOL : produces some metrics based on molecule
% -Averaged position among paired ones
% -TP as long as one there is one pairing
% Written by Thanh-an Pham, 2016
try
pairings = csvread([fpath, filesep, result_fname]);
catch
warning('No ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/assessment_main_automatic.m | .m | 9,678 | 223 | %% ASSESSMENT PROGRAM (MAIN) FOR AUTOMATIC RUN
% ASSESSMENT SCRIPT written by Thanh-an Pham (EPFL): 12-Jul-2016
% Expect standardized input files in folder 'participant_name/standard'
% converted by participant-specific converter script "convert_(participant_name).m"
%% Initialisation for for boucle
clear
res_fold = 'a... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/saveastiff.m | .m | 12,013 | 303 | function res = saveastiff(data, path, options)
% options.color
% : true or FALSE
% : If this is true, third dimension should be 3 and the data is saved as a color image.
% options.compress
% : 'no', 'lzw', 'jpeg' or 'adobe'.
% Compression type.
% 'no' : Uncompressed(Default)
% 'lzw' : lossles... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/boxrotate.m | .m | 643 | 24 | function [ newloc,ind ] = boxrotate(loc,orig,fov)
%BOXROTATE Summary of this function goes here
% Detailed explanation goes here
shift = orig + fov/2;
thetaxy = -deg2rad(6.35);
thetaxz = -deg2rad(5.08);
dn = 0;
Rxy = [cos(thetaxy),-sin(thetaxy),0;sin(thetaxy),cos(thetaxy),0;0,0,1];
Rxz = [cos(thetaxz),0,sin(thetaxz)... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/dispOrthoView.m | .m | 2,362 | 87 | function [h,hsub] = dispOrthoView(str_title,loc,gt,rad, varargin)
%Display an orthoview
% Either loc and gt are list of particle (frame, X, Y, Z)
% or cell containing the 3D image in the following way:
% {XYZ},{YZ},{XZ},{XY}
% When drawing rectangle, origin at bottom left
do2D = false;doRect = fals... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/main_plot3D.m | .m | 7,115 | 246 | %% Load pairings file resulting from assessment program
clear pos
path = '~/Dropbox/smlm/figures/';
%Winners:
%2D LD 3D-DAOSTORM
%2D HD SMfit
%AS LD CSpline
%AS HD SMolPhot
%BP LD MIATool
%BP HD ThunderSTORM
%DH LD CSpline
%DH HD CSpline
software = 'CSpline';%'TVSTORM';%'CSpline';%'3D-WTM';%'MIATool-RMS';%'STORMChaser'... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/gather_public.m | .m | 971 | 30 | %% Gather public.csv files to publics.csv
res_fold = 'assessment_results';
modality = {'AS','BP','DH','2D'};
folders = dir(res_fold);
folders = folders(4:end);
for k = 1:folders
for l = 1:length(modality)
fid = fopen([res_fold filesep folders(k) filesep modality{l}]);
nCol = fgetl(fid);
nCo... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/save_in_parfor.m | .m | 315 | 12 | function save_in_parfor(fullname,struct2save)
%SAVEVAR To use save in parfor loop
% INPUTS
% fullname : full filename (no .mat at the end)
% struct2save : save all the fields as separate variable
% save violates transparency in parallel computing
save([fullname,'.mat'],'-struct','struct2save','-v7.3');
end
| MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/make_cmp.m | .m | 6,850 | 167 | res_all = readtable('assessment_results/results_all.csv');
for n = 1:length(res_all.Properties.VariableNames)
units.(res_all.Properties.VariableNames{n}) = [];
end
%Manual Setting
crit_oi = {'Wob_'};
Ncategories = 2;
%'DeltaX','DeltaY','FRC_xy','MAD_lat','SNR_xy','RMSE_lat','Jaccard','Correl_'
metric = {'Jaccard'... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/getSigma.m | .m | 944 | 40 | function sig = getSigma(sigmin,sigmax,loc,k)
%GETSIGMA
%[V,C] = voronoin(unique(loc,'rows'));
%sig = zeros(length(C),1);
%for kk = 1:length(C)
%if isfinite(V(C{kk}))
%try
%[~,sig(kk)] = convhulln(V(C{kk},:));
%catch
% [~,sig(kk)] = convhulln(V(C{kk},:),{'Qt','Pp'});
% ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/main_random.m | .m | 882 | 29 | clear fov
nframes = [151,19620,3020,20000,3125,20120,3020];
fov{1} = [12800,12800,1500];
fov{2} = [6400,6400,1500];
datasets = {'Beads','ER1.N3.LD','ER2.N3.HD','MT1.N1.LD',...
'MT2.N1.HD','MT3.N2.LD','MT4.N2.HD'};
mod = {'AS','2D','DH','BP','DHNPC'};
if ~exist('RANDOM','dir')
mkdir('RANDOM','upload');
end
fo... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/assessment_graph.m | .m | 25,736 | 492 | function out = assessment_graph(filenames,varargin)
%ASSESSMENT_GRAPH : Create distribution of GT & TP wrt various variables
%and with different settings; wobble and pairing criterion (2D or 3D) curr.
% Common features among compared results
% -One participant
% -One dataset
% -One modality
% -One intensity thr... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/assessment_graph_old.m | .m | 20,600 | 414 | function out = assessment_graph_old(filenames,varargin)
%ASSESSMENT_GRAPH : Create distribution of GT & TP wrt various variables
%and with different settings; wobble and pairing criterion (2D or 3D) curr.
% Common features among compared results
% -One participant
% -One dataset
% -One modality
% -One intensity... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/disp3D.m | .m | 3,550 | 84 | function [fig,circSize,color,loc] = disp3D(loc,str_title,im3D,pix_siz)
%im3D (3D gaussian rendered localizations) and pix_siz will define circle
doProj = [true,false];
maxSize = 6;
minSize = 2;
fig = cell(2,1);
for imType = 1:2
sizIm = size(im3D);
fov = sizIm*pix_siz;
corrZ = fov(3)/2;
ind_rm = lo... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/importPublicRes.m | .m | 3,994 | 109 | function public = importPublicRes(filename, startRow, endRow)
%IMPORTFILE Import numeric data from a text file as a matrix.
% PUBLIC = IMPORTFILE(FILENAME) Reads data from text file FILENAME for
% the default selection.
%
% PUBLIC = IMPORTFILE(FILENAME, STARTROW, ENDROW) Reads data from rows
% STARTROW through ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_TVSTORM.m | .m | 6,513 | 173 | %% FILE STANDARDISATION : TVSTORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'TVSTORM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vec... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_3DWTM.m | .m | 6,813 | 178 | %% FILE STANDARDISATION : 3D-WTM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = '3D-WTM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vecto... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_CEL0.m | .m | 7,017 | 182 | %% FILE STANDARDISATION : CEL0
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'CEL0';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vector : ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_FIRESTORM.m | .m | 6,821 | 178 | %% FILE STANDARDISATION : FIRESTORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'FIRESTORM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_localizer.m | .m | 6,825 | 178 | %% FILE STANDARDISATION : localizer
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'localizer';%participant name
% user related parameters
sep = ' ';%' ';%separator type
%2 element... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_ThunderSTORM.m | .m | 6,533 | 173 | %% FILE STANDARDISATION : ThunderSTORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'ThunderSTORM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 el... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_HeaHD_deprecated.m | .m | 4,617 | 134 | %% FILE STANDARDISATION NO BEADS : HeaHD
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'HeaHD';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 element... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_ALOHA.m | .m | 4,633 | 134 | %% FILE STANDARDISATION NO BEADS : ALOHA
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'ALOHA';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 element... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_QCSTORMbeads.m | .m | 7,023 | 182 | %% FILE STANDARDISATION : QC-STORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'QC-STORM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements v... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_WaveTracer_old.m | .m | 4,460 | 130 | %% FILE STANDARDISATION NO BEADS : WaveTracer
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'WaveTracer';%participant name
% user related parameters
sep = '';%' ';%separator type
... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_Brecs.m | .m | 4,634 | 134 | %% FILE STANDARDISATION NO BEADS : Brecs
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'Brecs';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 element... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_L1H.m | .m | 4,441 | 129 | %% FILE STANDARDISATION NO BEADS : L1H
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
% user related parameters
sep = '';%' ';%separator type
%2 elements vector : [2D, others], if 1D => for all
param... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_MIATool.m | .m | 6,817 | 178 | %% FILE STANDARDISATION : MiaTool-RMS
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'MIATool';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_QCSTORM.m | .m | 4,635 | 134 | %% FILE STANDARDISATION NO BEADS : QC-STORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'QC-STORM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 e... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_MIAToolJAC.m | .m | 6,821 | 178 | %% FILE STANDARDISATION : MiaTool-RMS
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'MIATool-JAC';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elem... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_GT.m | .m | 6,807 | 178 | %% FILE STANDARDISATION : GT
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'GT';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vector : [2D,... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_STORMChaser.m | .m | 8,249 | 224 | %% FILE STANDARDISATION : STORMChaser
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
%%% Special convert here because intensity column available in one file %%%
clear
participant_name = 'STORMChaser';%part... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_localizer_SS.m | .m | 6,831 | 178 | %% FILE STANDARDISATION : localizer_SS
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'localizer_SS';%participant name
% user related parameters
sep = ' ';%' ';%separator type
%2 e... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_SMAP.m | .m | 7,017 | 182 | %% FILE STANDARDISATION : SMAP
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'SMAP';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vector : ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_localizer_GLRT.m | .m | 6,835 | 178 | %% FILE STANDARDISATION : localizer_GLRT
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'localizer_GLRT';%participant name
% user related parameters
sep = ' ';%' ';%separator type
... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_Octane.m | .m | 6,815 | 178 | %% FILE STANDARDISATION : Octane
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'Octane';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vecto... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_PeakFit_MLEC.m | .m | 6,828 | 178 | %% FILE STANDARDISATION : PeakFit_MLEC
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'PeakFit_MLEC';%participant name
% user related parameters
sep = ' ';%' ';%separator type
%2 e... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_BaselineLocalization.m | .m | 6,843 | 178 | %% FILE STANDARDISATION : BaselineLocalization
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'BaselineLocalization';%participant name
% user related parameters
sep = '';%' ';%sepa... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_QuickPALM.m | .m | 6,821 | 178 | %% FILE STANDARDISATION : QuickPALM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'QuickPALM';%participant name
% user related parameters
sep = ' ';%' ';%separator type
%2 element... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_MIAToolRMS.m | .m | 6,821 | 178 | %% FILE STANDARDISATION : MiaTool-RMS
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'MIATool-RMS';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elem... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_RainSTORM.m | .m | 6,825 | 178 | %% FILE STANDARDISATION : RainSTORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'RainSTORM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_3DSTORMTools.m | .m | 6,825 | 178 | %% FILE STANDARDISATION : 3D-STORM-Tools
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = '3D-STORM-Tools';%participant name
% user related parameters
sep = '';%' ';%separator type
%... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_WTM.m | .m | 6,463 | 173 | %% FILE STANDARDISATION : WTM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'WTM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vector : [2... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_PeakFit_LSE.m | .m | 6,826 | 178 | %% FILE STANDARDISATION : PeakFit_LSE
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'PeakFit_LSE';%participant name
% user related parameters
sep = ' ';%' ';%separator type
%2 ele... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_RapidSTORM.m | .m | 6,834 | 178 | %% FILE STANDARDISATION : RapidSTORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'RapidSTORM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elemen... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_mlePALM.m | .m | 7,028 | 182 | %% FILE STANDARDISATION : mlePALM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'mlePALM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vec... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_easyDH.m | .m | 6,812 | 179 | %% FILE STANDARDISATION : EasyDH
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'EasyDH';%participant name
% user related parameters
sep = [];%' ';%separator type
%2 elements vecto... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_SMfit.m | .m | 7,016 | 182 | %% FILE STANDARDISATION : SMfit
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'SMfit';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vector ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_model_no_beads.m | .m | 4,653 | 134 | %% FILE STANDARDISATION NO BEADS : INSERT_PARTICIPANT_NAME
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'SMAP';%participant name
% user related parameters
sep = '';%' ';%separato... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_RANDOM.m | .m | 6,813 | 178 | %% FILE STANDARDISATION : RANDOM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'RANDOM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vecto... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_SOLAR_STORM.m | .m | 6,602 | 173 | %% FILE STANDARDISATION : SOLAR_STORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'SOLAR_STORM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elem... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_3DDAOSTORM.m | .m | 6,824 | 179 | %% FILE STANDARDISATION : 3D-DAOSTORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = '3D-DAOSTORM';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elem... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_FALCON.m | .m | 4,650 | 134 | %% FILE STANDARDISATION NO BEADS : INSERT_PARTICIPANT_NAME
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'FALCON';%participant name
% user related parameters
sep = '';%' ';%separa... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_CSpline.m | .m | 4,462 | 129 | %% FILE STANDARDISATION NO BEADS : CSpline
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
% user related parameters
sep = '';%' ';%separator type
%2 elements vector : [2D, others], if 1D => for all
p... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_NeuralSTORM.m | .m | 4,640 | 134 | %% FILE STANDARDISATION NO BEADS : NeuralSTORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'NeuralSTORM';%participant name
% user related parameters
sep = '';%' ';%separator typ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_WaveTracer.m | .m | 7,030 | 182 | %% FILE STANDARDISATION : WaveTracer
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'WaveTracer';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elemen... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_MiaLang.m | .m | 6,815 | 178 | %% FILE STANDARDISATION : MiaLang
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'MiaLang';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vec... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_model.m | .m | 7,060 | 182 | %% FILE STANDARDISATION : INSERT_PARTICIPANT_NAME
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'INSERT_PARTICIPANT_NAME';%participant name
% user related parameters
sep = '';%' '... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_ADCG.m | .m | 6,805 | 178 | %% FILE STANDARDISATION : ADCG
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'ADCG';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vector : ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_PeakSelector.m | .m | 6,830 | 178 | %% FILE STANDARDISATION : PeakSelector
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'PeakSelector';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 el... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_PhasorThunderSTORM.m | .m | 7,044 | 182 | %% FILE STANDARDISATION : Phasor-ThunderSTORM
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'Phasor-ThunderSTORM';%participant name
% user related parameters
sep = '';%' ';%separa... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/old_convert_SMAP.m | .m | 4,629 | 134 | %% FILE STANDARDISATION NO BEADS : SMAP
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'SMAP';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_EasyDHPSF.m | .m | 6,818 | 178 | %% FILE STANDARDISATION : EasyDHPSF
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'EasyDHPSF';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_SFP_Estimator.m | .m | 6,828 | 178 | %% FILE STANDARDISATION : SFP_Estimator
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'SFP_Estimator';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_PeakFit_MLE.m | .m | 6,826 | 178 | %% FILE STANDARDISATION : PeakFit_MLE
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'PeakFit_MLE';%participant name
% user related parameters
sep = ' ';%' ';%separator type
%2 ele... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_SMolPhot.m | .m | 4,504 | 130 | %% FILE STANDARDISATION NO BEADS : SMolPhot
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'SMolPhot';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 e... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_SMAPRMS.m | .m | 4,637 | 134 | %% FILE STANDARDISATION NO BEADS : SMAP-RMS
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'SMAP-RMS';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 e... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/converter/convert_PALMER.m | .m | 6,813 | 178 | %% FILE STANDARDISATION : PALMER
% Specific to each participant, standardised output file saved in csv
% format : Dataset Localisation & Beads localisation standard format in
% 'standard' folder
clear
participant_name = 'PALMER';%participant name
% user related parameters
sep = '';%' ';%separator type
%2 elements vecto... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/colormap/morgenstemning.m | .m | 7,649 | 211 | function cmap=morgenstemning(n,varargin)
%MORGENSTEMNING Colormap that increases linearly in lightness (with colors)
%
% Written by Matthias Geissbuehler - matthias.geissbuehler@a3.epfl.ch
% January 2013
%
% Colormap that increases linearly in lightness (such as a pure black to white
% map) but incorporates additio... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/colormap/isolum.m | .m | 6,441 | 175 | function cmap=isolum(n,varargin)
%ISOLUM Isoluminant-Colormap compatible with red-green color perception deficiencies
%
% Written by Matthias Geissbuehler - matthias.geissbuehler@a3.epfl.ch
% January 2013
%
% Features:
% 1) All colors have the same luminescence (ideal for lifetime
% images that will be dis... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/colormap/ametrine.m | .m | 6,033 | 167 | function cmap=ametrine(n,varargin)
%AMETRINE "Nearly" isoluminant-Colormap compatible with red-green color perception deficiencies
%
% Written by Matthias Geissbuehler - matthias.geissbuehler@a3.epfl.ch
% January 2013
%
% Features:
% 1) All colors have the same luminescence (ideal for lifetime
% images tha... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/finddriftfeature.m | .m | 9,491 | 343 | function [drift,driftinfo]=finddriftfeature(pos,par)
global SMAP_stopnow
%pos.xnm .ynm .frame
%frame starts with 1, ascending order, maybe not necessary?
% XXX locData: sort function, general
% parameters and typical values (please adopt)
% par.drift_pixrec=15; %pixelsize of reconstructed images in nm
% par.drift_windo... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/finddriftfeatureZ.m | .m | 6,455 | 264 | function [drift,driftinfo]=finddriftfeatureZ(pos,par)
global SMAP_stopnow
%pos.xnm .ynm .znm .frame
%frame starts with 1, ascending order, maybe not necessary?
% XXX locData: sort function, general
% parameters and typical values (please adopt)
% par.drift_pixrec=15; %pixelsize of reconstructed images in nm
% par.drif... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/applydriftcorrection.m | .m | 1,314 | 32 | function poso=applydriftcorrection(drift,pos)
%pos: localizations with fields xnm ynm znm frame
indg=pos.frame>0;
if isfield(drift,'xy')
poso.xnm=pos.xnm;
poso.ynm=pos.ynm;
% for k=1:length(drit.xy)
if isfield(drift.xy(1),'x')
if strcmp(drift.xy(1).mirror,'horizontal')&&length(drift.xy... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/driftcorrection3D_so.m | .m | 3,726 | 100 | function drift=driftcorrection3D_so(x,y,z,frame,p)
pard.correctxy=true; %correct in x, y
pard.drift_timepoints=10; %number of time points (blocks) in x,y,
pard.drift_pixrec=5; %size of pixels for reconstruction (in units of x,y, e.g. nm)
pard.drift_window=7; %Size of window in which maximum of cross-correlation is foun... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/private/robustMean.m | .m | 4,397 | 155 | function [finalMean, stdSample, inlierIdx, outlierIdx] = robustMean(data,dim,k,fit)
%ROBUSTMEAN calculates mean and standard deviation discarding outliers
%
% SYNOPSIS [finalMean, stdSample, inlierIdx, outlierIdx] = robustMean(data,dim,k,fit)
%
% INPUT data : input data
% dim : (opt) dimension along which ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/private/initaxis.m | .m | 1,231 | 57 | function [ax,tab]=initaxis(handle,name,option)
if nargin<3
option='';
end
if isa(handle,'matlab.ui.container.Tab')
tab=handle;
ax=tab.Children;
tabgroup=tab.Parent;
% state=tab.Parent.Parent.Visible;
if ~strcmp(option,'keep')
delete(handle.Children(:));
handle.Title=name;
ax=ax... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/private/mypeakfit.m | .m | 77 | 4 | function [xpos,fp]=mypeakfit(x,y)
fp=polyfit(x,y,2);
xpos=-fp(2)/2/fp(1);
end | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/private/copyfields.m | .m | 1,131 | 47 | function [destination,missing]=copyfields(destination,source,fields)
missing={};
if nargin==2 %copy all
if ~isempty(source)
if isa(destination,'handle')
fn=intersect(properties(destination),fieldnames(source));
else
fn=fieldnames(source);
end
for k=1:length(fn... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/private/histrenderc.c | .c | 2,900 | 114 | #include "mex.h"
#include <stdio.h>
//#include <math.h>
/*void correlate(double *n1, double *G, mwSize lenG, mwSize lenn)*/
double gaussrender(float *srim,float *xpix, float *ypix, mwSize *srec, float *sigma, float *Gtemplate, float Gsigma, float roiks, float *N, int uselut, float *c, float *lut, float *rangec, mw... | C |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/private/finddisplacementZ.m | .m | 1,290 | 62 | function zpos=finddisplacementZ(xr,zr,xt,zt,xb,zb,window,plotaxis)
if nargin<8
plotaxis=[];
end
if nargin<7
window=[];
end
[~,sindr]=sort(xr);
[~,sindt]=sort(xt);
x1r=1;x1t=1;
ccc=zeros(1,length(zb)*2-3);
for k=1:length(xb)-1
x2r=x1r;x2t=x1t;
while(xr(sindr(x2r))<xb(k+1))&&x2r<length(sindr)
x2r=x... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/private/copystructReduce.m | .m | 353 | 14 | function destination=copystructReduce(source,ind,fn)
if ~isempty(source)
if nargin<3
fn=fieldnames(source);
end
for k=1:length(fn)
if length(ind)==length(source.(fn{k}))||~islogical(ind)
destination.(fn{k})=source.(fn{k})(ind);
else
destination.(fn{k})=source.... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/private/histrender.m | .m | 3,631 | 115 | function [srim,nlocs,template]=histrender(pos,rangex, rangey, pixelsx, pixelsy, lut,rangec,template)
%pos.x, pos.y, pos.c, pos.N,pos.s
%global variables
if isfield(pos,'N')
N=pos.N;
else
N=ones(length(pos.x),1,'like',pos.x);
end;
if isfield(pos,'s')
spix=pos.s/pixelsx;
else
spix=0*pos.x+120;
end
roiks=2... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/driftCorrection/private/my2Dgaussfit.m | .m | 9,042 | 344 | function [fitpos,outim,outimnorm,ci]=my2Dgaussfit(image,startp,cas)
%fit par=(x,y,a,bg,sx,sy,r)
if nargin<3
cas=2;
show=false;
end
if nargout>1
show=true;
end
% if ishandle(show)
% hfig=show;
% show=true;
% elseif show
% hf=figure(2);
% hfig=axes('Parent',hf);
% end
% %normalize by max pixel... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/wobble/simBeadLocCorr.m | .m | 931 | 27 | function [xnm, ynm, frame_out] = simBeadLocCorr(xnm, ynm, frame, gt)
%In case of exceeding number of localizations wrt expected one, pick the closest ones to the
%bead positions, not improving the results (even worse).
%DEPRECATED, not used
warning('warning : the function simBeadLocCorr should not be called');
nBeads ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/wobble/wobbleCalibration.m | .m | 28,199 | 988 | function [wobbleMatrix] = wobbleCalibration(x,y,z,nBead,varargin)
% WOBBLECALIBRATION Generate correction data for z-dependent "wobble"
%
% MODIFIED BY THANH-AN 24th May 2016
%
% SYNTAX
% [wobbleMatrix]=wobbleCalibration(x,y,z,nBead)
% [wobbleMatrix]=wobbleCalibration(..., 'SaveWobbleFile',wobbleFileName)
% [wobbleM... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/wobble/wobbleCorrectSimBead.m | .m | 868 | 29 | function wobbleCorrectSimBead(xnm,ynm,frame,gt,zmin,zstep,zmax,roiRadius,fname)
nBead = size(gt,1);
for ii = 1:nBead
beadPos = gt(ii,:);
ROInm(ii,1:2) = beadPos-roiRadius;%xmin ymin
ROInm(ii,3:4) = 2*roiRadius;%width height
end
zSlice = zmin:zstep:zmax;
%frameIsOneIndexed = ~sum(frame==0) > 0;%should det... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/additionaluserinterface/SpinnerDouble.java | .java | 3,557 | 119 | //=========================================================================================
//
// Project: AdditionalUserInterface - Providing GUI for ImageJ plugin
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL)... | Java |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/additionaluserinterface/Settings.java | .java | 12,943 | 448 | //=========================================================================================
//
// Project: AdditionalUserInterface - Providing GUI for ImageJ plugin
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL)... | Java |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/additionaluserinterface/Chrono.java | .java | 1,854 | 64 | //=========================================================================================
//
// Project: AdditionalUserInterface - Providing GUI for ImageJ plugin
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL)... | Java |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/additionaluserinterface/GridPanel.java | .java | 4,211 | 169 | //=========================================================================================
//
// Project: AdditionalUserInterface - Providing GUI for ImageJ plugin
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL)... | Java |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/additionaluserinterface/SpinnerFloat.java | .java | 3,532 | 121 | //=========================================================================================
//
// Project: AdditionalUserInterface - Providing GUI for ImageJ plugin
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL)... | Java |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/additionaluserinterface/SpinnerInteger.java | .java | 3,538 | 119 | //=========================================================================================
//
// Project: AdditionalUserInterface - Providing GUI for ImageJ plugin
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL)... | Java |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/additionaluserinterface/WalkBar.java | .java | 10,257 | 323 | //=========================================================================================
//
// Project: AdditionalUserInterface - Providing GUI for ImageJ plugin
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL)... | Java |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/smlms/Description.java | .java | 1,854 | 64 | // =========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/smlms/CompareLocalization3DDialog.java | .java | 19,031 | 455 | //=========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
2D | SMLM-Challenge/Challenge2016 | Assessment/CompareLocalization3D/src/smlms/FluorophorePair.java | .java | 1,651 | 50 | //=========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
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