processExp : main function for running the segmentation software.
Used to choose the appropriate settings, and converting the images
filenames before running BatchSuperSeggerOpti.
Images need to have the NIS-Elements Format, or they can be converted
using convertImageNames.
the naming convention of the image files must be of the following format
time, xy-positions, fluorescence channel, where c1 is bright field
and c2,c3 etc are different fluorescent channels
Example of two time points, two xy positions and one fluorescent channel
filename_t001xy1c1.tif
filename_t001xy1c2.tif
filename_t001xy2c1.tif
filename_t001xy2c2.tif
filename_t002xy1c1.tif
filename_t002xy1c2.tif
filename_t002xy2c1.tif
filename_t002xy2c2.tif
INPUT :
dirname : folder that contains .tif images in NIS elements format.
Copyright (C) 2016 Wiggins Lab
Written by Paul Wiggins, Nathan Kuwada, Stella Stylianidou.
University of Washington, 2016
This file is part of SuperSegger.
SuperSegger 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 later version.
SuperSegger is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with SuperSegger. If not, see <http://www.gnu.org/licenses/>.0001 function processExp( dirname ) 0002 % processExp : main function for running the segmentation software. 0003 % Used to choose the appropriate settings, and converting the images 0004 % filenames before running BatchSuperSeggerOpti. 0005 % Images need to have the NIS-Elements Format, or they can be converted 0006 % using convertImageNames. 0007 % 0008 % the naming convention of the image files must be of the following format 0009 % time, xy-positions, fluorescence channel, where c1 is bright field 0010 % and c2,c3 etc are different fluorescent channels 0011 % Example of two time points, two xy positions and one fluorescent channel 0012 % filename_t001xy1c1.tif 0013 % filename_t001xy1c2.tif 0014 % filename_t001xy2c1.tif 0015 % filename_t001xy2c2.tif 0016 % filename_t002xy1c1.tif 0017 % filename_t002xy1c2.tif 0018 % filename_t002xy2c1.tif 0019 % filename_t002xy2c2.tif 0020 % 0021 % INPUT : 0022 % dirname : folder that contains .tif images in NIS elements format. 0023 % 0024 % 0025 % Copyright (C) 2016 Wiggins Lab 0026 % Written by Paul Wiggins, Nathan Kuwada, Stella Stylianidou. 0027 % University of Washington, 2016 0028 % This file is part of SuperSegger. 0029 % 0030 % SuperSegger is free software: you can redistribute it and/or modify 0031 % it under the terms of the GNU General Public License as published by 0032 % the Free Software Foundation, either version 3 of the License, or 0033 % (at your option) any later version. 0034 % 0035 % SuperSegger is distributed in the hope that it will be useful, 0036 % but WITHOUT ANY WARRANTY; without even the implied warranty of 0037 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 0038 % GNU General Public License for more details. 0039 % 0040 % You should have received a copy of the GNU General Public License 0041 % along with SuperSegger. If not, see <http://www.gnu.org/licenses/>. 0042 0043 %% Converting other microscopes files 0044 % For example if you are using MicroManager and the file format is the 0045 % followin : date-strain_00000000t_BF.tif, date-strain_00000000t_GFP.tif, 0046 % you can run convertImageNames(dirname, 'whatever_name_you_want', '', 't', 0047 % '','', {'BF','GFP'} ) 0048 0049 basename = 'date-strain'; 0050 timeFilterBefore ='t'; 0051 timeFilterAfter = '_' ; 0052 xyFilterBefore='_x'; 0053 xyFilterAfter='_'; 0054 channelNames = {'BF','GFP'}; 0055 0056 convertImageNames(dirname, basename, timeFilterBefore, ... 0057 timeFilterAfter, xyFilterBefore,xyFilterAfter, channelNames ) 0058 0059 %% Set the segmentations constants for your bacteria and micrscope resolution 0060 % Using correct resolution ensures correct pixel size and segmentation constants 0061 % if you do not know which constants to use you can run 0062 % tryDifferentConstants(dirname) with a phase image to choose. 0063 % 60X indicates 100nm/pix and 100X indicates 60nm/pix 0064 0065 % for E. coli we mainly use : 0066 % '60XEc' : loadConstants 60X Ecoli - 100 nm/pix 0067 % '100XEc': loadConstants 100X Ecoli - 60 nm/pix 0068 0069 % To see the possible constants type : 0070 %[~, list] = getConstantsList; 0071 % list' 0072 0073 res = '60XEcLB'; 0074 0075 %% Paralell Processing Mode 0076 % to run code in parallel mode must have the parallel processing toolbox, 0077 % for convenience default is false (non-parallel) 0078 0079 parallel_flag = false; 0080 0081 %% Load Constants 0082 CONST = loadConstants(res,parallel_flag) ; 0083 0084 %% Calculation Options 0085 % after you load the constants you can modify them according to your needs 0086 % for more options, looks at the loadConstants file. 0087 0088 CONST.trackLoci.numSpots = [5 0]; % Max number of foci to fit in each fluorescence channel (default = [0 0]) 0089 CONST.trackLoci.fluorFlag = false ; % compute integrated fluorescence (default = true) 0090 CONST.trackOpti.NEIGHBOR_FLAG = false; % calculate number of neighbors (default = false) 0091 CONST.imAlign.AlignChannel = 1; % change this if you want the images to be aligned to fluorescence channel 0092 0093 0094 %% Skip Frames for Segmentation 0095 % For fast time-lapse or slow growth you can skip phase image frames 0096 % during segmentation to increase processing speed. Fluorescence images 0097 % will not be skipped. 0098 0099 skip = 1; % segment every frame 0100 %skip = 5; % segment every fifth phase image 0101 0102 %% Clean previous segmented data 0103 % If set to true, will begin processing on aligned images; if false, will 0104 % try to restart processing at last successful function (default = false) 0105 0106 cleanflag = false; 0107 0108 0109 %% Start running segmentation 0110 0111 BatchSuperSeggerOpti( dirname, skip, cleanflag, CONST); 0112 0113 0114 end