Commit e1738ede authored by Balint Balazs's avatar Balint Balazs
Browse files

adds comments to scripts in paper_figures folder

parent 44fa1f22
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% Generate Figure 1c for B³D compression paper %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 27.06.2017 %
% EMBL Heidelberg, Cell Biology and Biophysics %
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%% define data
baseFolder = fileparts(matlab.desktop.editor.getActiveFilename);
......
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% Simulate blinking fluorophores on a regular grid %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 15.05.2017 %
% EMBL Heidelberg, Cell Biology and Biophysics %
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%% Parameters
spacing = 21.1; % fluorophore spacing
gridSize = 10; % grid size
......
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% Simulating SMLM experiments with various SNR
% Author: Balint Balazs
% contact: balint.balazs@embl.de
% 23.06.2017
% EMBL Heidelberg, Cell Biology and Biophysics
%
%
% NPhtoons = (100,500,1000,5000,10000,50000)
% BGPhotons = 20 for all
% Generate Figure 2 and Supplementary Figure 6 for B³D paper %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 23.06.2017 %
% EMBL Heidelberg, Cell Biology and Biophysics %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear variables;
%%
......
/*
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Prepare stacks for segmentation %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 23.06.2017 %
% EMBL Heidelberg, Cell Biology and Biophysics %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
*/
baseFolder = "D:\\GPU_compression\\!paper_figures\\Fig_2_drosophila\\"
files = newArray("drosophila_1_masked24_1024x2048x211_filtered.h5")
//datasets = newArray("B3D_1.0", "B3D_3.0","B3D_swapped_1.0", "B3D_swapped_3.0")
......
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% Compare segmentation of original and BD compressed images %
% Compare segmentation of original and B³D compressed images %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 23.06.2017 %
......
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Generate Supplementary Figure 2c,d for B³D paper %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 27.06.2017 %
% EMBL Heidelberg, Cell Biology and Biophysics %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear variables;
%%
baseFolder = 'D:\GPU_compression\!paper_figures\SFig_2_swapping\';
......
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% Generate Supplementary Figure 2a,b for B³D paper %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 27.06.2017 %
% EMBL Heidelberg, Cell Biology and Biophysics %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear variables;
%%
baseFolder = 'D:\GPU_compression\!paper_figures\SFig_2_swapping\';
......
/*
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% Generate subfigures for Supplementary Figure 3 for B³D paper %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 27.06.2017 %
% EMBL Heidelberg, Cell Biology and Biophysics %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
*/
run("Scriptable load HDF5...", "load=D:\\GPU_compression\\!paper_figures\\SFig_3_imageQuality\\drosophila_1_masked24_1024x2048x211_filtered.h5 datasetnames=/B3D_0.00 nframes=1 nchannels=1");
rename("lossless");
run("Duplicate...", "title=lossless-194 duplicate range=194-194");
......
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% Compare image noise level with BD compression artifacts %
% Compare image noise level with B³D compression artifacts %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 26.06.2016 %
......
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 10 11:33:10 2017
@author: Balint Balazs
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% Batch compression of Phallusia images for Supplementary Figure 5 %
% for B³D paper %
% Author: Balint Balazs %
% contact: balint.balazs@embl.de %
% 28.06.2017 %
% EMBL Heidelberg, Cell Biology and Biophysics %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
"""
......
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