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value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
|---|---|---|---|---|---|---|---|---|
github | mehta-lab/Instantaneous-PolScope-master | overlayPositionOrientation.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/overlayPositionOrientation.m | 9,980 | utf_8 | ef6930d0f6004cdd62ddcf79d3c20649 | function [movOrient,hAxisOverlay,hAxisIntensity,xstart,ystart,xend,yend]=overlayPositionOrientation(xPart,yPart,anisoPart,orientPart,intPart,polstack,varargin)
% [movOrient,hAxisOverlay,hAxisIntensity,xstart,ystart,xend,yend]=overlayPositionOrientation(xPart,yPart,anisoPart,orientPart,intPart,polstack,varargin)
% Funct... |
github | mehta-lab/Instantaneous-PolScope-master | exportHyperStack.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/exportHyperStack.m | 2,931 | utf_8 | 456d02abfb6eb940fa93b8e6412c4906 | function exportHyperStack(stackData, filename,varargin)
% exportHyperStack(stackData, filename) exports multi-D data as ImageJ
% hyperstack assuming XYCZT order of the dimensions.
% Usage:
% teststack=zeros(100,100,8,5,'uint16');
% exportHyperStack(teststack,'test_hyperstack.tif');
%
%
% arg=parsepropval(arg,varargin{... |
github | mehta-lab/Instantaneous-PolScope-master | TIFFStack.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/@TIFFStack/TIFFStack.m | 13,989 | utf_8 | 287162d4012fbcbc09fd0bf123b35837 | % TIFFStack - Manipulate a TIFF file like a tensor
%
% Usage: tsStack = TIFFStack(strFilename <, bInvert>)
%
% A TIFFStack object behaves like a read-only memory mapped TIF file. The
% entire image stack is treated as a matlab tensor. Each frame of the file must
% have the same dimensions. Reading the image data i... |
github | mehta-lab/Instantaneous-PolScope-master | tiffread29_header.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/@TIFFStack/private/tiffread29_header.m | 14,865 | utf_8 | 35a2408a96acaa8010a29500dba775cf | function [TIF, HEADER] = tiffread29_header(filename)
%% set defaults values :
TIF.BOS = 'ieee-le'; %byte order string
TIF.strFilename = filename;
consolidateStrips = true;
if isempty(findstr(filename,'.'))
filename = [filename,'.tif'];
end
TIF.file = fopen(filename,'r','l');
if TIF.file == ... |
github | mehta-lab/Instantaneous-PolScope-master | tiffread29_readimage.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/@TIFFStack/private/tiffread29_readimage.m | 4,906 | utf_8 | f3afa2f5e5294c9f00734aecee2a8473 | function [data, stack] = tiffread29_readimage(TIF, HEADER, vnFrames)
% - Preallocate data block
classname = get_data_class(HEADER(vnFrames(1)), 1);
data = zeros(HEADER(vnFrames(1)).height, HEADER(vnFrames(1)).width, numel(vnFrames), HEADER(vnFrames(1)).SamplesPerPixel, classname);
stack = [];
for (nFrame = numel(vnFr... |
github | mehta-lab/Instantaneous-PolScope-master | calibReg.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/@RTFluorPol/calibReg.m | 12,545 | utf_8 | 256ebdffb16c8ef50c262cdac506894f | function calibReg(self,Ireg,varargin)
% calibReg(RTFluorPolObject,Ireg,'Property','value')
% Property Possible values (Default in bracket)
% 'regMethod' ('manual'),'matlab','phasecor','reset'
% 'preProcReg' ('none'),'lowpass','edge'
% 'diagnosis' (true), false.
% 'regType' 'translation',('rigid'),'simila... |
github | mehta-lab/Instantaneous-PolScope-master | normQuadsManual.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/@RTFluorPol/normQuadsManual.m | 6,995 | utf_8 | 9880601af4ef3fad717be211366a5a14 | function normQuadsManual(self,I0,I45,I90,I135,varargin)
% normQuadsManual(RTFluorPol Object,I0,I45,I90,I135,'Parameter',value)
% Optional arguments
% Parameter Value
% 'normRange' 2-value vector [minNorm maxNorm].
% 'normROI' Isotropic ROI known to have low anisotropy.
%% Assign defa... |
github | mehta-lab/Instantaneous-PolScope-master | regQuadsManual.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/@RTFluorPol/regQuadsManual.m | 13,131 | utf_8 | 037412c4de5c13229fefb3d3ca2e5cba | function regQuadsManual(self,I0,I45,I90,I135,varargin)
% [tformI45,tformI90,tformI135]=regQuadsManual(I0,I45,I90,I135)
% Optional arguments
% Parameter Value
% 'ShiftRange' 2-value vector [minshift maxshift] in pixels.
% 'RotationRange' 2-value vector [minrotation maxrotation] in deg.
% 'S... |
github | mehta-lab/Instantaneous-PolScope-master | screencapture.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/screencapture.m | 34,159 | utf_8 | d79cc0eed8f03127f0825954b69cf72b | function imageData = screencapture(varargin)
% screencapture - get a screen-capture of a figure frame, component handle, or screen area rectangle
%
% ScreenCapture gets a screen-capture of any Matlab GUI handle (including desktop,
% figure, axes, image or uicontrol), or a specified area rectangle located relative to
%... |
github | mehta-lab/Instantaneous-PolScope-master | gridfit.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/gridfit.m | 33,939 | utf_8 | a1f046d6cbc834284e6954d5a30dcaf4 | function [zgrid,xgrid,ygrid] = gridfit(x,y,z,xnodes,ynodes,varargin)
% gridfit: estimates a surface on a 2d grid, based on scattered data
% Replicates are allowed. All methods extrapolate to the grid
% boundaries. Gridfit uses a modified ridge estimator to
% generate the surface, where the bi... |
github | mehta-lab/Instantaneous-PolScope-master | distance2curve.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/distance2curve.m | 55,860 | utf_8 | eda95809c753c165dd4f72f49b652555 | function [xy,distance,t_a] = distance2curve(curvexy,mapxy,interpmethod)
% distance2curve: minimum distance from a point to a general curvilinear n-dimensional arc
% usage: [xy,distance,t] = distance2curve(curvexy,mapxy) % uses linear curve segments
% usage: [xy,distance,t] = distance2curve(curvexy,mapxy,interpmethod)
%... |
github | mehta-lab/Instantaneous-PolScope-master | myginput.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/myginput.m | 6,466 | utf_8 | cd9eb5958c608e8178bfbfdc400c1b9d | function [out1,out2,out3] = myginput(arg1,strpointertype)
%MYGINPUT Graphical input from mouse with custum cursor pointer.
% [X,Y] = MYGINPUT(N) gets N points from the current axes and returns
% the X- and Y-coordinates in length N vectors X and Y.
%
% [X,Y] = MYGINPUT(N, POINTER) also specifies the cursor point... |
github | mehta-lab/Instantaneous-PolScope-master | pdftops.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/pdftops.m | 3,574 | utf_8 | 92ff676904575e16046dfff010b4e145 | function varargout = pdftops(cmd)
%PDFTOPS Calls a local pdftops executable with the input command
%
% Example:
% [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for future refere... |
github | mehta-lab/Instantaneous-PolScope-master | crop_borders.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/crop_borders.m | 3,666 | utf_8 | ebb9c61581b6f0d4a2db2fd1d9e30685 | function [A, vA, vB, bb_rel] = crop_borders(A, bcol, padding)
%CROP_BORDERS Crop the borders of an image or stack of images
%
% [B, vA, vB, bb_rel] = crop_borders(A, bcol, [padding])
%
%IN:
% A - HxWxCxN stack of images.
% bcol - Cx1 background colour vector.
% padding - scalar indicating how much padding to ha... |
github | mehta-lab/Instantaneous-PolScope-master | isolate_axes.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/isolate_axes.m | 4,721 | utf_8 | 253cd7b7d8fc7cb00d0cc55926f32de5 | function fh = isolate_axes(ah, vis)
%ISOLATE_AXES Isolate the specified axes in a figure on their own
%
% Examples:
% fh = isolate_axes(ah)
% fh = isolate_axes(ah, vis)
%
% This function will create a new figure containing the axes/uipanels
% specified, and also their associated legends and colorbars. The objects
%... |
github | mehta-lab/Instantaneous-PolScope-master | im2gif.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/im2gif.m | 6,048 | utf_8 | 5a7437140f8d013158a195de1e372737 | %IM2GIF Convert a multiframe image to an animated GIF file
%
% Examples:
% im2gif infile
% im2gif infile outfile
% im2gif(A, outfile)
% im2gif(..., '-nocrop')
% im2gif(..., '-nodither')
% im2gif(..., '-ncolors', n)
% im2gif(..., '-loops', n)
% im2gif(..., '-delay', n)
%
% This function converts a mu... |
github | mehta-lab/Instantaneous-PolScope-master | read_write_entire_textfile.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/read_write_entire_textfile.m | 924 | utf_8 | 779e56972f5d9778c40dee98ddbd677e | %READ_WRITE_ENTIRE_TEXTFILE Read or write a whole text file to/from memory
%
% Read or write an entire text file to/from memory, without leaving the
% file open if an error occurs.
%
% Reading:
% fstrm = read_write_entire_textfile(fname)
% Writing:
% read_write_entire_textfile(fname, fstrm)
%
%IN:
% fname - Pathn... |
github | mehta-lab/Instantaneous-PolScope-master | pdf2eps.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/pdf2eps.m | 1,471 | utf_8 | a1f41f0c7713c73886a2323e53ed982b | %PDF2EPS Convert a pdf file to eps format using pdftops
%
% Examples:
% pdf2eps source dest
%
% This function converts a pdf file to eps format.
%
% This function requires that you have pdftops, from the Xpdf suite of
% functions, installed on your system. This can be downloaded from:
% http://www.foolabs.com/xpdf ... |
github | mehta-lab/Instantaneous-PolScope-master | print2array.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/print2array.m | 9,369 | utf_8 | ca18a1e6c5a944b591a0557bd69f1c2c | function [A, bcol] = print2array(fig, res, renderer, gs_options)
%PRINT2ARRAY Exports a figure to an image array
%
% Examples:
% A = print2array
% A = print2array(figure_handle)
% A = print2array(figure_handle, resolution)
% A = print2array(figure_handle, resolution, renderer)
% A = print2array(figure_handle... |
github | mehta-lab/Instantaneous-PolScope-master | append_pdfs.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/append_pdfs.m | 2,678 | utf_8 | 949c7c4ec3f5af6ff23099f17b1dfd79 | %APPEND_PDFS Appends/concatenates multiple PDF files
%
% Example:
% append_pdfs(output, input1, input2, ...)
% append_pdfs(output, input_list{:})
% append_pdfs test.pdf temp1.pdf temp2.pdf
%
% This function appends multiple PDF files to an existing PDF file, or
% concatenates them into a PDF file if the output fi... |
github | mehta-lab/Instantaneous-PolScope-master | using_hg2.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/using_hg2.m | 1,002 | utf_8 | b1620dd31f4d0b8acea2723e354a3518 | %USING_HG2 Determine if the HG2 graphics engine is used
%
% tf = using_hg2(fig)
%
%IN:
% fig - handle to the figure in question.
%
%OUT:
% tf - boolean indicating whether the HG2 graphics engine is being used
% (true) or not (false).
% 19/06/2015 - Suppress warning in R2015b; cache result for improved per... |
github | mehta-lab/Instantaneous-PolScope-master | eps2pdf.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/eps2pdf.m | 7,661 | utf_8 | ab0c84a2a57942e7e121faef8e0742df | function eps2pdf(source, dest, crop, append, gray, quality, gs_options)
%EPS2PDF Convert an eps file to pdf format using ghostscript
%
% Examples:
% eps2pdf source dest
% eps2pdf(source, dest, crop)
% eps2pdf(source, dest, crop, append)
% eps2pdf(source, dest, crop, append, gray)
% eps2pdf(source, dest, crop... |
github | mehta-lab/Instantaneous-PolScope-master | export_fig.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/export_fig.m | 54,007 | utf_8 | 32f46fe89fce17e6b2e57b732facbcf6 | function [imageData, alpha] = export_fig(varargin)
%EXPORT_FIG Exports figures in a publication-quality format
%
% Examples:
% imageData = export_fig
% [imageData, alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... -transparent
% ex... |
github | mehta-lab/Instantaneous-PolScope-master | ghostscript.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/ghostscript.m | 7,492 | utf_8 | 7a1e094c8bf153e1b239765ff6fd43df | function varargout = ghostscript(cmd)
%GHOSTSCRIPT Calls a local GhostScript executable with the input command
%
% Example:
% [status result] = ghostscript(cmd)
%
% Attempts to locate a ghostscript executable, finally asking the user to
% specify the directory ghostcript was installed into. The resulting path
% is s... |
github | mehta-lab/Instantaneous-PolScope-master | fix_lines.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/export_fig/fix_lines.m | 6,290 | utf_8 | 8437006b104957762090e3d875688cb6 | %FIX_LINES Improves the line style of eps files generated by print
%
% Examples:
% fix_lines fname
% fix_lines fname fname2
% fstrm_out = fixlines(fstrm_in)
%
% This function improves the style of lines in eps files generated by
% MATLAB's print function, making them more similar to those seen on
% screen. Grid ... |
github | mehta-lab/Instantaneous-PolScope-master | movieDataGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/movieDataGUI.m | 14,080 | utf_8 | 4dd1aefb597084a14d2c9a2ce779d250 | function varargout = movieDataGUI(varargin)
% MOVIEDATAGUI M-file for movieDataGUI.fig
% MOVIEDATAGUI, by itself, creates a new MOVIEDATAGUI or raises the existing
% singleton*.
%
% H = MOVIEDATAGUI returns the handle to a new MOVIEDATAGUI or the handle to
% the existing singleton*.
%
% MOVIEDA... |
github | mehta-lab/Instantaneous-PolScope-master | speckleDetectionProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/speckleDetectionProcessGUI.m | 9,854 | utf_8 | d31a208bcf8ea2c7e83c1e42c2ec9bf5 | function varargout = speckleDetectionProcessGUI(varargin)
% speckleDetectionProcessGUI M-file for speckleDetectionProcessGUI.fig
% speckleDetectionProcessGUI, by itself, creates a new speckleDetectionProcessGUI or raises the existing
% singleton*.
%
% H = speckleDetectionProcessGUI returns the handle to ... |
github | mehta-lab/Instantaneous-PolScope-master | flowTrackingProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/flowTrackingProcessGUI.m | 9,499 | utf_8 | 33dffc0df71fa3ab79a0a90c1c389e95 | function varargout = flowTrackingProcessGUI(varargin)
% flowTrackingProcessGUI M-file for flowTrackingProcessGUI.fig
% flowTrackingProcessGUI, by itself, creates a new flowTrackingProcessGUI or raises the existing
% singleton*.
%
% H = flowTrackingProcessGUI returns the handle to a new flowTrackingProces... |
github | mehta-lab/Instantaneous-PolScope-master | channelGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/channelGUI.m | 11,289 | utf_8 | 97d5a872f8f89ea40a13945e3f1e05ca | function varargout = channelGUI(varargin)
% CHANNELGUI M-file for channelGUI.fig
% CHANNELGUI, by itself, creates a new CHANNELGUI or raises the existing
% singleton*.
%
% H = CHANNELGUI returns the handle to a new CHANNELGUI or the handle to
% the existing singleton*.
%
% CHANNELGUI('CALLBACK'... |
github | mehta-lab/Instantaneous-PolScope-master | MovieObject.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/MovieObject.m | 19,558 | utf_8 | a2b7ca9100db285b63292955b45073f5 | classdef MovieObject < hgsetget
% Abstract interface defining the analyis tools for movie objects
% (movies, movie lists...)
%
% Copyright (C) 2012 LCCB
%
% This file is part of QFSM.
%
% QFSM is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as pu... |
github | mehta-lab/Instantaneous-PolScope-master | name2wavelength.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/name2wavelength.m | 1,153 | utf_8 | 0efaabaf9f7d5ef9e5e515d6108b4e87 |
% Francois Aguet, 06/30/2011
%
% Copyright (C) 2012 LCCB
%
% This file is part of QFSM.
%
% QFSM is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any la... |
github | mehta-lab/Instantaneous-PolScope-master | buildSpeckleArray.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/buildSpeckleArray.m | 25,002 | utf_8 | 099861ab75967e7988a43815b3b12218 | function speckleArray=buildSpeckleArray(cM,noiseParams,threshold,gapList,cands,img,varargin)
% buildSpeckleArray fills the speckleArray structure containing all speckle information extracted from the analysis of an FSM stack
%
% SYNOPSIS speckleArray=buildSpeckleArray(cM,noiseParams,threshold)
%
% INPUT cM ... |
github | mehta-lab/Instantaneous-PolScope-master | FlowTrackingProcess.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/FlowTrackingProcess.m | 6,583 | utf_8 | b9294d2d10e6b023c4400a274137942a | classdef FlowTrackingProcess < ImageAnalysisProcess
% Concrete class for a flow tracking process
%
% Sebastien Besson, 5/2011
%
% Copyright (C) 2012 LCCB
%
% This file is part of QFSM.
%
% QFSM is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License a... |
github | mehta-lab/Instantaneous-PolScope-master | thresholdProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/thresholdProcessGUI.m | 21,191 | utf_8 | d710bf7e77b09cc1171ba4987714f3a6 | function varargout = thresholdProcessGUI(varargin)
% thresholdProcessGUI M-file for thresholdProcessGUI.fig
% thresholdProcessGUI, by itself, creates a new thresholdProcessGUI or raises the existing
% singleton*.
%
% H = thresholdProcessGUI returns the handle to a new thresholdProcessGUI or the handle to... |
github | mehta-lab/Instantaneous-PolScope-master | scaleContrast.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/scaleContrast.m | 1,274 | utf_8 | 70c0faf19d14ebc348658a403b510f03 | %out = scaleContrast(in, rangeIn, rangeOut) adjusts the contrast of the input
%
% Inputs:
% in : input signal
% rangeIn : input range. If empty, [min(in(:)) max(in(:))]
% rangeOut : output range
%
% Copyright (C) 2012 LCCB
%
% This file is part of QFSM.
%
% QFSM is free software: you can redistribute it ... |
github | mehta-lab/Instantaneous-PolScope-master | bfImport.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/bfImport.m | 7,619 | utf_8 | 5581d593bf14dfe54fb8f3b97368d297 | function MD = bfImport(dataPath,varargin)
% BFIMPORT imports movie files into MovieData objects using Bioformats
%
% MD = bfimport(dataPath)
%
% Load proprietary files using the Bioformats library. Read the metadata
% that is associated with the movie and the channels and set them into the
% created movie objects. Opt... |
github | mehta-lab/Instantaneous-PolScope-master | userfcn_saveCheckbox.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/userfcn_saveCheckbox.m | 1,227 | utf_8 | b479fb471c7dc40b23b23dc1ff0f48d3 |
function checked = userfcn_saveCheckbox(handles)
% GUI tool function - return the check/uncheck status of checkbox of
% processes in package control panel
%
% Input:
%
% handles - the "handles" of package control panel movie
%
% Output:
%
% checked - array of check/unchecked status 1 - checked, 0 - unchecke... |
github | mehta-lab/Instantaneous-PolScope-master | msgboxGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/msgboxGUI.m | 5,702 | utf_8 | a6b41c4b0e091b74b0b4568dbc79b336 | function varargout = msgboxGUI(varargin)
% MSGBOXGUI M-file for msgboxGUI.fig
% MSGBOXGUI, by itself, creates a new MSGBOXGUI or raises the existing
% singleton*.
%
% H = MSGBOXGUI returns the handle to a new MSGBOXGUI or the handle to
% the existing singleton*.
%
% MSGBOXGUI('CALLBACK',hObject... |
github | mehta-lab/Instantaneous-PolScope-master | plotScaleBar.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/plotScaleBar.m | 3,905 | utf_8 | d298498fbdcc4d3c5a5f154b781bcc02 | %plotScaleBar(width, varargin) adds a scale bar to a figure.
%
% Inputs: width : width of the scale bar, in x-axis units.
% h : axes handle. If empty, current axes ('gca') are used.
% varargin : optional inputs, always in name/value pairs:
% 'Location' : {'NorthEast', 'SouthEast', '... |
github | mehta-lab/Instantaneous-PolScope-master | cropMovieGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/cropMovieGUI.m | 13,292 | utf_8 | f1df0ac075f95cc1798e8c14dc2159f6 | function varargout = cropMovieGUI(varargin)
% cropMovieGUI M-file for cropMovieGUI.fig
% cropMovieGUI, by itself, creates a new cropMovieGUI or raises the existing
% singleton*.
%
% H = cropMovieGUI returns the handle to a new cropMovieGUI or the handle to
% the existing singleton*.
%
% cropMov... |
github | mehta-lab/Instantaneous-PolScope-master | padarrayXT.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/padarrayXT.m | 9,977 | utf_8 | b5dfc4e9473b41fe46216ba08a849299 | function b = padarrayXT(varargin)
%PADARRAYXT Modified version of built-in function 'padarray'.
% Mirroring ('symmetric' option) does not duplicate the border pixel.
% B = PADARRAYXT(A,PADSIZE) pads array A with PADSIZE(k) number of zeros
% along the k-th dimension of A. PADSIZE should be a vector of
% nonnega... |
github | mehta-lab/Instantaneous-PolScope-master | getFluorPropStruct.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/getFluorPropStruct.m | 2,135 | utf_8 | 0c9e124473a898979cc7662fb1aed3af | % Values from http://www.olympusfluoview.com/applications/fpcolorpalette.html
% Alexa Fluors: http://www.invitrogen.com/site/us/en/home/References/Molecular-Probes-The-Handbook/Technical-Notes-and-Product-Highlights/The-Alexa-Fluor-Dye-Series.html
%
% Copyright (C) 2012 LCCB
%
% This file is part of QFSM.
%
% QFSM is... |
github | mehta-lab/Instantaneous-PolScope-master | trackStackFlow.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/trackStackFlow.m | 27,283 | utf_8 | fe2a7c5655b0d3cfc4c4cfc2acdfe370 | function [v,corLength,sigtVal] = trackStackFlow(stack,points,minCorL,varargin)
%trackStackFlow: Calculate the flow velocity from a stack of movie images.
%
% SYNOPSIS :
% v = trackStackFlow(stack,points,minCorL)
% [v,corLen] = trackStackFlow(stack,points,minCorL,maxCorL,varargin)
% [v,corLen,sigtVal] = trackSt... |
github | mehta-lab/Instantaneous-PolScope-master | trackSpeckles.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/trackSpeckles.m | 6,284 | utf_8 | 10061247bfb8da2fca4fe503ec8c4fba | function [M vectors]=trackSpeckles(I,J,threshold, varargin)
% trackSpeckles uses the interpolated vector field to refine the tracking
%
% SYNOPSIS M = trackSpeckles(I,J,threshold)
% M = trackSpeckles(I,J,threshold,'initM',initM,'initCorLen',initCorLen)
%
% INPUT I : matrix [y x I]n of speckle... |
github | mehta-lab/Instantaneous-PolScope-master | maskRefinementProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/maskRefinementProcessGUI.m | 10,611 | utf_8 | 65f2c327d142bed6240e167c2cbf915c | function varargout = maskRefinementProcessGUI(varargin)
% MASKREFINEMENTPROCESSGUI M-file for maskRefinementProcessGUI.fig
% MASKREFINEMENTPROCESSGUI, by itself, creates a new MASKREFINEMENTPROCESSGUI or raises the existing
% singleton*.
%
% H = MASKREFINEMENTPROCESSGUI returns the handle to a new MASKRE... |
github | mehta-lab/Instantaneous-PolScope-master | MakeQTMovie.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/MakeQTMovie.m | 29,830 | utf_8 | 285b3b909f0c5edc95258c1daa5e3117 | function MakeQTMovie(cmd,arg, arg2)
% function MakeQTMovie(cmd, arg, arg2)
% Create a QuickTime movie from a bunch of figures (and an optional sound).
%
% Syntax: MakeQTMovie cmd [arg]
% The following commands are supported:
% addfigure - Add snapshot of current figure to movie
% addaxes - Add snapshot of current axes... |
github | mehta-lab/Instantaneous-PolScope-master | recycleProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/recycleProcessGUI.m | 9,804 | utf_8 | a88bb2d4f5b018d7fb9eeabf2b2c51c9 | function varargout = recycleProcessGUI(varargin)
% RECYCLEPROCESSGUI M-file for recycleProcessGUI.fig
% RECYCLEPROCESSGUI, by itself, creates a new RECYCLEPROCESSGUI or raises the existing
% singleton*.
%
% H = RECYCLEPROCESSGUI returns the handle to a new RECYCLEPROCESSGUI or the handle to
% the ex... |
github | mehta-lab/Instantaneous-PolScope-master | flowAnalysisProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/flowAnalysisProcessGUI.m | 7,426 | utf_8 | 940863cc8f0156d649fa7d33edb728b5 | function varargout = flowAnalysisProcessGUI(varargin)
% flowAnalysisProcessGUI M-file for flowAnalysisProcessGUI.fig
% flowAnalysisProcessGUI, by itself, creates a new flowAnalysisProcessGUI or raises the existing
% singleton*.
%
% H = flowAnalysisProcessGUI returns the handle to a new flowAnalysisProces... |
github | mehta-lab/Instantaneous-PolScope-master | userfcn_checkAllMovies.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/userfcn_checkAllMovies.m | 2,862 | utf_8 | 6a100db6360cdf72ed28a3fd31dece47 | function userfcn_checkAllMovies(procID, value, handles)
if get(handles.checkbox_all, 'Value')
userData = get(handles.figure1, 'UserData');
for x = setdiff(1:length(userData.MD), userData.id)
% Recalls the userData that may have been updated by the
% checkAllMovies function
%
% Copyright (C... |
github | mehta-lab/Instantaneous-PolScope-master | movieSelectorGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/movieSelectorGUI.m | 17,862 | utf_8 | 55b8091f6b801ba061cedf901dcdc2ef | function varargout = movieSelectorGUI(varargin)
% MOVIESELECTORGUI M-file for movieSelectorGUI.fig
% MOVIESELECTORGUI, by itself, creates a new MOVIESELECTORGUI or raises the existing
% singleton*.
%
% H = MOVIESELECTORGUI returns the handle to a new MOVIESELECTORGUI or the handle to
% the existing ... |
github | mehta-lab/Instantaneous-PolScope-master | trackSpecklesGapCloser.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/trackSpecklesGapCloser.m | 25,186 | utf_8 | ccb0557af7abf183da3707242a5dd994 | function [M,gapList]=trackSpecklesGapCloser(M,threshold,invalidCands,varargin)
% fsmTrackgapCloser closes gaps in speckles lifetimes by recovering weak
% local maxima close (in space and time) to a birth and death event
%
% SYNOPSIS [M,gapClosed]=fsmTrackGapCloser(M,threshold,strg,userPath,firstIndex,frame)
%
% IN... |
github | mehta-lab/Instantaneous-PolScope-master | processGUI_OpeningFcn.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/processGUI_OpeningFcn.m | 9,135 | utf_8 | 3d6bce13e58298f8d84b38e07a0aebdc | function processGUI_OpeningFcn(hObject, eventdata, handles, string,varargin)
% Common initialization of concrete process GUIs
%
% This function fills various fields of the userData
% userData.mainFig - handle to the main figure
% userData.handles_main - 'handles' of main figure
% userData.procID - Th... |
github | mehta-lab/Instantaneous-PolScope-master | detectSpeckles.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/detectSpeckles.m | 17,854 | utf_8 | c6568f7101403d3a5d1728d5d68606e2 | function [cands locMax]=detectSpeckles(I,noiseParam,specParam,varargin)
% detectSpeckles detects speckles in a filtered image
%
% Plots PSFs on the positions of the primary speckles (found by locmax operator) and substructs
% them from the filtered data. Appled again on the resulting image, the locmax-operator finds
... |
github | mehta-lab/Instantaneous-PolScope-master | movieViewer.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/movieViewer.m | 45,341 | utf_8 | 32495b017b0dc3a8c372e825f97f74e2 | function mainFig = movieViewer(MO,varargin)
ip = inputParser;
ip.addRequired('MO',@(x) isa(x,'MovieObject'));
ip.addOptional('procId',[],@isnumeric);
ip.addParamValue('movieIndex',0,@isscalar);
ip.parse(MO,varargin{:});
% Check existence of viewer
%
% Copyright (C) 2012 LCCB
%
% This file is part of QFSM.
%
% QFSM ... |
github | mehta-lab/Instantaneous-PolScope-master | dataPreparationGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/dataPreparationGUI.m | 29,435 | utf_8 | 638addd5f5871857e30fecde23d77197 | function varargout = dataPreparationGUI(varargin)
% DATAPREPARATIONGUI M-file for dataPreparationGUI.fig
% DATAPREPARATIONGUI, by itself, creates a new DATAPREPARATIONGUI or raises the existing
% singleton*.
%
% H = DATAPREPARATIONGUI returns the handle to a new DATAPREPARATIONGUI or the handle to
% ... |
github | mehta-lab/Instantaneous-PolScope-master | SpeckleTrackingProcess.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/SpeckleTrackingProcess.m | 7,543 | utf_8 | 163e1c767e01d3fcf82d99c838c61985 | classdef SpeckleTrackingProcess < DataProcessingProcess
% Concrete class for a speckle tracking process
%
% Sebastien Besson, May 2011
%
% Copyright (C) 2012 LCCB
%
% This file is part of QFSM.
%
% QFSM is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public ... |
github | mehta-lab/Instantaneous-PolScope-master | packageGUI_RunFcn.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/packageGUI_RunFcn.m | 13,383 | utf_8 | f9131d2eae6da6949f0b386c4646a0d1 | function packageGUI_RunFcn(hObject,eventdata,handles)
% Run the selected processes in the packageGUI interface
%
% This is a common section of code called by pushbutton_run_Callback
% when user click the "Run" button on package control panels.
%
% Copyright (C) 2012 LCCB
%
% This file is part of QFSM.
%
% QFSM is fre... |
github | mehta-lab/Instantaneous-PolScope-master | abstractProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/abstractProcessGUI.m | 6,409 | utf_8 | 3a28b0e14f1fe7bd34e4ae1cd28a936c | function varargout = abstractProcessGUI(varargin)
%ABSTRACTPROCESSGUI M-file for abstractProcessGUI.fig
% ABSTRACTPROCESSGUI, by itself, creates a new ABSTRACTPROCESSGUI or raises the existing
% singleton*.
%
% H = ABSTRACTPROCESSGUI returns the handle to a new ABSTRACTPROCESSGUI or the handle to
% ... |
github | mehta-lab/Instantaneous-PolScope-master | naFromLensID.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/naFromLensID.m | 3,457 | utf_8 | f4c3286efd85be69065b29f69e0ffebc | function [NA,mag] = naFromLensID(lensID,ask)
%NAFROMLENSID is a lookup table to find the NA for a given lensID
%
% SYNOPSIS [NA,mag] = naFromLensID(lensID,ask)
%
% INPUT lensID : ID of the lens according to deltaVision
% ask : Whether or not to ask for lensID if not found in list
% ... |
github | mehta-lab/Instantaneous-PolScope-master | kineticAnalysisProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/kineticAnalysisProcessGUI.m | 6,620 | utf_8 | f2ebaf86cf423d3507559c4d3066c031 | function varargout = kineticAnalysisProcessGUI(varargin)
% kineticAnalysisProcessGUI M-file for kineticAnalysisProcessGUI.fig
% kineticAnalysisProcessGUI, by itself, creates a new kineticAnalysisProcessGUI or raises the existing
% singleton*.
%
% H = kineticAnalysisProcessGUI returns the handle to a new ... |
github | mehta-lab/Instantaneous-PolScope-master | packageGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/packageGUI.m | 10,750 | utf_8 | 42cfd7447b909a06314f77ffab3a1cdd | function varargout = packageGUI(varargin)
% PACKAGEGUI M-file for packageGUI.fig
% PACKAGEGUI, by itself, creates a new PACKAGEGUI or raises the existing
% singleton*.
%
% H = PACKAGEGUI returns the handle to a new PACKAGEGUI or the handle to
% the existing singleton*.
%
% PACKAGEGUI('CALLBACK'... |
github | mehta-lab/Instantaneous-PolScope-master | getGaussianPSFsigma.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/getGaussianPSFsigma.m | 2,763 | utf_8 | aebaaeedecd4b414ab7081ad95d1de1d | % getGaussianPSFsigma returns the standard deviation of the Gaussian
% approximation of an ideal PSF in pixel
%
% INPUTS NA : numerical aperture of the objective
% M : magnification of the objective
% pixelSize : physical pixel size of the CCD in [m]
% lambda : emi... |
github | mehta-lab/Instantaneous-PolScope-master | addMovieROIGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/addMovieROIGUI.m | 11,121 | utf_8 | 3ee82ad3e76273b9b28c52ff1a12b064 | function varargout = addMovieROIGUI(varargin)
% addMovieROIGUI M-file for addMovieROIGUI.fig
% addMovieROIGUI, by itself, creates a new addMovieROIGUI or raises the existing
% singleton*.
%
% H = addMovieROIGUI returns the handle to a new addMovieROIGUI or the handle to
% the existing singleton*.
%
... |
github | mehta-lab/Instantaneous-PolScope-master | packageGUI_OpeningFcn.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/packageGUI_OpeningFcn.m | 13,491 | utf_8 | fdc2c582da0d11e09581745185284f0d | function packageGUI_OpeningFcn(hObject,eventdata,handles,packageName,varargin)
% Callback called at the opening of packageGUI
%
% packageGUI_OpeningFcn(packageName,MD) MD: MovieData object
%
% Useful tools
%
% User Data:
%
% userData.MD - array of MovieData object
% userData.MD - array of MovieList object... |
github | mehta-lab/Instantaneous-PolScope-master | speckleTrackingProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/speckleTrackingProcessGUI.m | 7,441 | utf_8 | 190b2d54085c54b30e00c5a6d5762040 | function varargout = speckleTrackingProcessGUI(varargin)
% speckleTrackingProcessGUI M-file for speckleTrackingProcessGUI.fig
% speckleTrackingProcessGUI, by itself, creates a new speckleTrackingProcessGUI or raises the existing
% singleton*.
%
% H = speckleTrackingProcessGUI returns the handle to a new ... |
github | mehta-lab/Instantaneous-PolScope-master | noiseEstimationProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/noiseEstimationProcessGUI.m | 12,506 | utf_8 | 6ef97ab21e7de79888eaa2a480673103 | function varargout = noiseEstimationProcessGUI(varargin)
% noiseEstimationProcessGUI M-file for noiseEstimationProcessGUI.fig
% noiseEstimationProcessGUI, by itself, creates a new noiseEstimationProcessGUI or raises the existing
% singleton*.
%
% H = noiseEstimationProcessGUI returns the handle to a new ... |
github | mehta-lab/Instantaneous-PolScope-master | trackMovieSpeckles.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/trackMovieSpeckles.m | 9,305 | utf_8 | 7b6cd7625f476968da8367efc7d648ce | function trackMovieSpeckles(movieData,varargin)
% trackMovieSpeckles tracks the speckles of a movie
%
% Copyright (C) 2012 LCCB
%
% This file is part of QFSM.
%
% QFSM is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Fou... |
github | mehta-lab/Instantaneous-PolScope-master | bfGetPlane.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/qFSM/bio-formats/bfGetPlane.m | 3,316 | utf_8 | 23879b4ca68d2da2bd94c99c43608811 | function I = bfGetPlane(r, iPlane)
% Get the plane data from a dataset reader using bioformats tools
%
% SYNOPSIS I = bfGetPlane(r, iPlane)
%
% Input
% r - the reader object (e.g. the output bfGetReader)
%
% iPlane - a scalar giving the index of the plane to be retrieved.
%
% Output
%
% I - an array of size ... |
github | mehta-lab/Instantaneous-PolScope-master | bfCheckJavaPath.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/bioformats/bfCheckJavaPath.m | 3,237 | utf_8 | a8204822a04672d090a16a10d4e3bf12 | function [status, version] = bfCheckJavaPath(varargin)
% bfCheckJavaPath check Bio-Formats is included in the Java class path
%
% SYNOPSIS bfCheckJavaPath()
% status = bfCheckJavaPath(autoloadBioFormats)
% [status, version] = bfCheckJavaPath()
%
% Input
%
% autoloadBioFormats - Optional. A boole... |
github | mehta-lab/Instantaneous-PolScope-master | movieDataGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/movieDataGUI.m | 15,141 | utf_8 | 875ac3d79fa44477ad0f7d6595b6d6e7 | function varargout = movieDataGUI(varargin)
% MOVIEDATAGUI M-file for movieDataGUI.fig
% MOVIEDATAGUI, by itself, creates a new MOVIEDATAGUI or raises the existing
% singleton*.
%
% H = MOVIEDATAGUI returns the handle to a new MOVIEDATAGUI or the handle to
% the existing singleton*.
%
% MOVIEDA... |
github | mehta-lab/Instantaneous-PolScope-master | trackCloseGapsKalmanSparse.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/trackCloseGapsKalmanSparse.m | 36,873 | utf_8 | cb4935f9a7f8b4807975fa1681689161 | function [tracksFinal,kalmanInfoLink,errFlag] = trackCloseGapsKalmanSparse(...
movieInfo,costMatrices,gapCloseParam,kalmanFunctions,probDim,...
saveResults,verbose,varargin)
%TRACKCLOSEGAPSKALMANSPARSE (1) links features between frames, possibly using the Kalman Filter for motion propagation and (2) closes gaps... |
github | mehta-lab/Instantaneous-PolScope-master | anisoGaussianDetectionProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/anisoGaussianDetectionProcessGUI.m | 6,443 | utf_8 | b34bcd3e9886b156478d8f96eb21502c | function varargout = anisoGaussianDetectionProcessGUI(varargin)
% anisoGaussianDetectionProcessGUI M-file for anisoGaussianDetectionProcessGUI.fig
% anisoGaussianDetectionProcessGUI, by itself, creates a new anisoGaussianDetectionProcessGUI or raises the existing
% singleton*.
%
% H = anisoGaussianDetect... |
github | mehta-lab/Instantaneous-PolScope-master | plusTipWithinGroupComparison.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/plusTipWithinGroupComparison.m | 4,350 | utf_8 | b4feab4eb44a303b3744a234858080f3 | function plusTipWithinGroupComparison(groupData, iGroup, varargin)
% plusTipPoolGroupData pools plus tip data from multiple projects in groups
%
% SYNOPSIS: plusTipWithinGroupComparison(groupData, saveDir, doPlot)
%
% INPUT:
% groupList : output of plusTipExtractGroupData, nProj x 2 cell array
% saveDir : path to ou... |
github | mehta-lab/Instantaneous-PolScope-master | omeroImport.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/omeroImport.m | 5,645 | utf_8 | bb25155593f450c02de931d1e2a3b566 | function movie = omeroImport(session,imageID,varargin)
% OMEROIMPORT imports images from an OMERO server into MovieData objects
%
% movie = omeroImport(session)
%
% Load proprietary files using the Bioformats library. Read the metadata
% that is associated with the movie and the channels and set them into the
% created... |
github | mehta-lab/Instantaneous-PolScope-master | setErrorbarStyle.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/setErrorbarStyle.m | 1,541 | utf_8 | eb7025ae7b73d5766e40031c35701343 | %setErrorbarStyle(he, pos, de) modifies the width of the error bars
%
% Copyright (C) 2014 LCCB
%
% This file is part of u-track.
%
% u-track is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 ... |
github | mehta-lab/Instantaneous-PolScope-master | movieViewerOptions.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/movieViewerOptions.m | 18,609 | utf_8 | 6aa52eea4a33069fc3257a65c57f719d | function optionsFig = movieViewerOptions(mainFig)
%GRAPHVIEWER creates a graphical interface to control the movie options
%
% This function creates a list of checkboxes for all graph processes which
% output can be displayed in a standalone figure. It is called by
% movieViewer.
%
% Input
%
% mainFig - the handle o... |
github | mehta-lab/Instantaneous-PolScope-master | channelGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/channelGUI.m | 11,799 | utf_8 | 60e2117986c079fbd5c6ccd59665e855 | function varargout = channelGUI(varargin)
% CHANNELGUI M-file for channelGUI.fig
% CHANNELGUI, by itself, creates a new CHANNELGUI or raises the existing
% singleton*.
%
% H = CHANNELGUI returns the handle to a new CHANNELGUI or the handle to
% the existing singleton*.
%
% CHANNELGUI('CALLBACK'... |
github | mehta-lab/Instantaneous-PolScope-master | readtiff.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/readtiff.m | 3,515 | utf_8 | 1a79d4a5da7da10b817709336b93042f | %[s] = readtiff(filepath) loads a tiff file or stack using libtiff
% This function is ~1.5-2x faster than imread, useful for large stacks,
% and supports a wider range of TIFF formats (see below)
%
% Inputs:
% filepath : path to TIFF file to read from
%
% Optional inputs
% range : range of pages to read from... |
github | mehta-lab/Instantaneous-PolScope-master | MovieObject.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/MovieObject.m | 22,005 | utf_8 | e063700a106112a9c5f638a15b120329 | classdef MovieObject < hgsetget
% Abstract interface defining the analyis tools for movie objects
% (movies, movie lists...)
%
% Copyright (C) 2014 LCCB
%
% This file is part of u-track.
%
% u-track is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License... |
github | mehta-lab/Instantaneous-PolScope-master | name2wavelength.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/name2wavelength.m | 1,165 | utf_8 | 3a11bd3adb07963539c72a3afad159c5 |
% Francois Aguet, 06/30/2011
%
% Copyright (C) 2014 LCCB
%
% This file is part of u-track.
%
% u-track is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) ... |
github | mehta-lab/Instantaneous-PolScope-master | plusTipCostMatCloseGapsGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/plusTipCostMatCloseGapsGUI.m | 5,937 | utf_8 | ba7fc8770c27a1ab83c384f0138f5f72 | function varargout = plusTipCostMatCloseGapsGUI(varargin)
% PLUSTIPCOSTMATCLOSEGAPSGUI M-file for plusTipCostMatCloseGapsGUI.fig
% PLUSTIPCOSTMATCLOSEGAPSGUI, by itself, creates a new PLUSTIPCOSTMATCLOSEGAPSGUI or raises the existing
% singleton*.
%
% H = PLUSTIPCOSTMATCLOSEGAPSGUI returns the handle to ... |
github | mehta-lab/Instantaneous-PolScope-master | pointSourceDetection.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/pointSourceDetection.m | 8,294 | utf_8 | d5139d79def0a3261e4193b3ae572fe1 | %[pstruct, mask, imgLM, imgLoG] = pointSourceDetection(img, sigma, mode)
%
% Inputs :
% img : input image
% sigma : standard deviation of the Gaussian PSF
%
% Options (as 'specifier'-value pairs):
%
% 'mode' : parameters to estimate. Default: 'xyAc'.
% 'alpha' ... |
github | mehta-lab/Instantaneous-PolScope-master | bfImport.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/bfImport.m | 9,330 | utf_8 | 449a51086b2423d8452b4b5886cca6b3 | function MD = bfImport(dataPath,varargin)
% BFIMPORT imports movie files into MovieData objects using Bioformats
%
% MD = bfimport(dataPath)
% MD = bfimport(dataPath, false)
% MD = bfimport(dataPath, 'outputDirectory', outputDir)
%
% Load proprietary files using the Bioformats library. Read the metadata
% that is assoc... |
github | mehta-lab/Instantaneous-PolScope-master | userfcn_saveCheckbox.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/userfcn_saveCheckbox.m | 1,238 | utf_8 | e39588a918fae19c1fcec72fe9fa2ead |
function checked = userfcn_saveCheckbox(handles)
% GUI tool function - return the check/uncheck status of checkbox of
% processes in package control panel
%
% Input:
%
% handles - the "handles" of package control panel movie
%
% Output:
%
% checked - array of check/unchecked status 1 - checked, 0 - unchecke... |
github | mehta-lab/Instantaneous-PolScope-master | msgboxGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/msgboxGUI.m | 5,815 | utf_8 | bb522a760915f439bbb09ed82ae26155 | function varargout = msgboxGUI(varargin)
% MSGBOXGUI M-file for msgboxGUI.fig
% MSGBOXGUI, by itself, creates a new MSGBOXGUI or raises the existing
% singleton*.
%
% H = MSGBOXGUI returns the handle to a new MSGBOXGUI or the handle to
% the existing singleton*.
%
% MSGBOXGUI('CALLBACK',hObject... |
github | mehta-lab/Instantaneous-PolScope-master | isSubclass.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/isSubclass.m | 2,097 | utf_8 | 3df6753cfcbfca84196cda5fc7a52ad9 | function status = isSubclass(classname,parentname)
%ISSUBCLASS check if a class inherits from a parent class
%
% Synopsis status = isSubclass(classname,parentname)
%
% Input:
% classname - a string giving the name of the class (child)
%
% parentname - a string giving the name of the parent class
%
% Output
% sta... |
github | mehta-lab/Instantaneous-PolScope-master | plotScaleBar.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/plotScaleBar.m | 4,008 | utf_8 | b7aeaf3895797ded1420a884739be339 | %plotScaleBar(width, varargin) adds a scale bar to a figure.
%
% Inputs: width : width of the scale bar, in x-axis units.
% h : axes handle. If empty, current axes ('gca') are used.
% varargin : optional inputs, always in name/value pairs:
% 'Location' : {'NorthEast', 'SouthEast', '... |
github | mehta-lab/Instantaneous-PolScope-master | costMatRandomDirectedSwitchingMotionCloseGapsGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/costMatRandomDirectedSwitchingMotionCloseGapsGUI.m | 14,630 | utf_8 | 95fb6a930421a0f524720e7a557648f1 | function varargout = costMatRandomDirectedSwitchingMotionCloseGapsGUI(varargin)
% COSTMATRANDOMDIRECTEDSWITCHINGMOTIONCLOSEGAPSGUI M-file for costMatRandomDirectedSwitchingMotionCloseGapsGUI.fig
% COSTMATRANDOMDIRECTEDSWITCHINGMOTIONCLOSEGAPSGUI, by itself, creates a new COSTMATRANDOMDIRECTEDSWITCHINGMOTIONCLOSEGA... |
github | mehta-lab/Instantaneous-PolScope-master | cropMovieGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/cropMovieGUI.m | 13,292 | utf_8 | 632f4b6f0da5496d9638d67fbc8a79de | function varargout = cropMovieGUI(varargin)
% cropMovieGUI M-file for cropMovieGUI.fig
% cropMovieGUI, by itself, creates a new cropMovieGUI or raises the existing
% singleton*.
%
% H = cropMovieGUI returns the handle to a new cropMovieGUI or the handle to
% the existing singleton*.
%
% cropMov... |
github | mehta-lab/Instantaneous-PolScope-master | padarrayXT.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/padarrayXT.m | 9,989 | utf_8 | 022c2f55f7cc19443f657a7222e4b65c | function b = padarrayXT(varargin)
%PADARRAYXT Modified version of built-in function 'padarray'.
% Mirroring ('symmetric' option) does not duplicate the border pixel.
% B = PADARRAYXT(A,PADSIZE) pads array A with PADSIZE(k) number of zeros
% along the k-th dimension of A. PADSIZE should be a vector of
% nonnega... |
github | mehta-lab/Instantaneous-PolScope-master | getFluorPropStruct.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/getFluorPropStruct.m | 2,343 | utf_8 | 73fa811827f9f106a7b9a1508776eab0 | % Values from http://www.olympusfluoview.com/applications/fpcolorpalette.html
% Alexa Fluors: http://www.invitrogen.com/site/us/en/home/References/Molecular-Probes-The-Handbook/Technical-Notes-and-Product-Highlights/The-Alexa-Fluor-Dye-Series.html
%
% Copyright (C) 2014 LCCB
%
% This file is part of u-track.
%
% u-tr... |
github | mehta-lab/Instantaneous-PolScope-master | barplot2.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/barplot2.m | 8,680 | utf_8 | da27be83188b815676132adcd89ea62b | %BARPLOT2 Bar plot grouping multiple sets/categories of data, with error bars.
%
% Inputs: prm : cell array of matrices that contain the box properties:
% row 1: height
% row 2: optional, error bars
% errorbars : cell array colors, each containing a Nx3 matrix. Colors cycle through... |
github | mehta-lab/Instantaneous-PolScope-master | cometDetection.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/cometDetection.m | 6,755 | utf_8 | 3aca3d6e6edfd49b3d8f8cf3af52dcc6 | % featuresInfo = cometDetection(img, mask, psfSigma, mode)
%
% Inputs : img : input image
% mask : cell mask
% psfSigma : standard deviation of the Gaussian PSF
% {mode} : parameters to estimate, default 'xyArtc'
% {alpha} : alpha-values for statistical test
% ... |
github | mehta-lab/Instantaneous-PolScope-master | motionAnalysisProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/motionAnalysisProcessGUI.m | 6,511 | utf_8 | b871bab1808e1cb74cf3eef8463fa479 | function varargout = motionAnalysisProcessGUI(varargin)
% motionAnalysisProcessGUI M-file for motionAnalysisProcessGUI.fig
% motionAnalysisProcessGUI, by itself, creates a new motionAnalysisProcessGUI or raises the existing
% singleton*.
%
% H = motionAnalysisProcessGUI returns the handle to a new motion... |
github | mehta-lab/Instantaneous-PolScope-master | HCSplatestack.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/HCSplatestack.m | 2,492 | utf_8 | 1c4f1b9bdb81b8abde6df30edef6e8d1 | function [chplatestack, starti, startsw] = HCSplatestack(varagin)
chplatestack = [];
dirurl = varagin;
file_lists = dir(fullfile(dirurl, '*.TIF')); ct = 0;
lenf = zeros(1, 10);
for i2 = 1:10
lenf(i2) = length(file_lists(i2).name); % see if there is inconsistent double digit naming
end
% if lenf(10) ~= mean(lenf)
% ... |
github | mehta-lab/Instantaneous-PolScope-master | MakeQTMovie.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/MakeQTMovie.m | 29,841 | utf_8 | 28412bad79f01471d852bd2dcda56185 | function MakeQTMovie(cmd,arg, arg2)
% function MakeQTMovie(cmd, arg, arg2)
% Create a QuickTime movie from a bunch of figures (and an optional sound).
%
% Syntax: MakeQTMovie cmd [arg]
% The following commands are supported:
% addfigure - Add snapshot of current figure to movie
% addaxes - Add snapshot of current axes... |
github | mehta-lab/Instantaneous-PolScope-master | cometPostTrackingProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/cometPostTrackingProcessGUI.m | 6,077 | utf_8 | 1adf2297da70584ca18a58d0f599e739 | function varargout = cometPostTrackingProcessGUI(varargin)
% cometPostTrackingProcessGUI M-file for cometPostTrackingProcessGUI.fig
% cometPostTrackingProcessGUI, by itself, creates a new cometPostTrackingProcessGUI or raises the existing
% singleton*.
%
% H = cometPostTrackingProcessGUI returns the hand... |
github | mehta-lab/Instantaneous-PolScope-master | recycleProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/recycleProcessGUI.m | 9,825 | utf_8 | 43449c3b28eb23b0d486c92d733b1342 | function varargout = recycleProcessGUI(varargin)
% RECYCLEPROCESSGUI M-file for recycleProcessGUI.fig
% RECYCLEPROCESSGUI, by itself, creates a new RECYCLEPROCESSGUI or raises the existing
% singleton*.
%
% H = RECYCLEPROCESSGUI returns the handle to a new RECYCLEPROCESSGUI or the handle to
% the ex... |
github | mehta-lab/Instantaneous-PolScope-master | filterLoG.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/filterLoG.m | 2,255 | utf_8 | 51664e4425e439e9812813f363b0391f | % filterLoG : filters a signal with a Laplacian of Gaussian filter. Unlike
% the built-in Matlab function fspecial('Laplacian'), this function computes
% the exact convolution, using FFTs.
%
% out = filterLoG(signal, sigma);
%
% INPUT: signal: input (1-3 dimensional)
% sigma : standard deviation of the ... |
github | mehta-lab/Instantaneous-PolScope-master | subResolutionProcessGUI.m | .m | Instantaneous-PolScope-master/MehtaetalPNAS2016/contrib/u-track-2.1.3/software/subResolutionProcessGUI.m | 17,501 | utf_8 | d8fdbd388e2db5d6d9da2032b35ed30e | function varargout = subResolutionProcessGUI(varargin)
% SUBRESOLUTIONPROCESSGUI M-file for subResolutionProcessGUI.fig
% SUBRESOLUTIONPROCESSGUI, by itself, creates a new SUBRESOLUTIONPROCESSGUI or raises the existing
% singleton*.
%
% H = SUBRESOLUTIONPROCESSGUI returns the handle to a new SUBRESOLUTIO... |
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