Description of ag

DESCRIPTION

 ag : autogain, it increases the contrast of image im, using imin and imax.
 It subtracts the the minimum from of the image, divides by the max and
 then normalizes to 255.

 INPUT : 
       im : image
       imin : min value used to set autogained image (default : min of image)
       imax : max value used to set autogained image (default : max of image)
 OUTPUT :
       im : autogained image with increased contrast.


 Copyright (C) 2016 Wiggins Lab 
 Written by Paul Wiggins.
 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/>.

CROSS-REFERENCE INFORMATION

trackOptiAlignPad trackOptiAlignPad : aligns phase images to correct for microscope drift.

trackOptiCropMulti trackOptiCropMulti : user chooses two corners to crops multiple images

tryDifferentConstants tryDifferentConstants : displays images of cells segmented with

toMakeCell toMakeCell : calls toMakeCellFast to calculate the properties of a cell.

trackOptiMakeCell trackOptiMakeCell : generates the CellA field indexed by the region number

displayMap intDisplay : displays linking - used for debugging.

errorRez errorRez : links cells from the frame before to the current and attempts to

errorRezNew errorRezNew : links cells from the frame before to the current and attempts to

missingSeg2to1 missingSeg2to1 : finds missing segment in regC.

splitAreaErrors splitAreaErrors : splits cells with large area error.

trackOptiStripSmall trackOptiStripSmall : removes small regions and fills holes in the regions.

gateMake gateMake : used to create a gate field in the clist.

cellprops3 cellprops3 : Calculates the shape properties of the region or 'cell'.

cellprops5 cellprops5 : Calculates the shape properties of a region or 'cell'.

defineGoodSegs defineGoodSegs sets the segments to good, bad and 3n set by the watershed algorithm

makeBgMask makeBgMask : makes a background mask for the phase image

perRegionOpti perRegionOpti : Segmentaion optimization using region characteristics.

regionOpti regionOpti : Segmentaion optimization using region characteristics.

superSeggerOpti superSeggerOpti generates the initial segmentation of rod-shaped cells.

systematic systematic: Finds the minimum energy configuration by trying all segment

showSegRule showSegRule : shows the segmentation for regions and segments

showSegRuleGUI showSegRule : shows the segmentation for regions and segments

colorize colorize : creates an image, with defined mask, colormap, and background

comp comp : creates composite image

makeCellMovie makeCellMovie : creates a movie for a single cell file

makeConsensusImage makeConsensusImage : Computes consensus fluorescence localization from cells in a cell files

makeFrameMosaic makeFrameMosaic: Creates a tower for a single cell.

makeKymoMosaic makeKymoMosaic creates a mosaic kymograph of multiple cells.

makeKymographC makeKymographC : creates a kymograph for given cell data file..

showCellOutline showCellOutline : draws the outlines for the regions in the data file.

showSegData showSegData : draws the outlines for the regions in the data file.

showSegDataPhase showSegDataPhase : draws the outlines for the regions in the data file.

showSeggerImage showSeggerImage : produces the superSeggerViewer image according to clist and

towerMergeImages towerMergeImages : merges the towers of several cells.

SOURCE CODE

0001 function [im,im_min,imax] = ag (im,imin,imax)
0002 % ag : autogain, it increases the contrast of image im, using imin and imax.
0003 % It subtracts the the minimum from of the image, divides by the max and
0004 % then normalizes to 255.
0005 %
0006 % INPUT :
0007 %       im : image
0008 %       imin : min value used to set autogained image (default : min of image)
0009 %       imax : max value used to set autogained image (default : max of image)
0010 % OUTPUT :
0011 %       im : autogained image with increased contrast.
0012 %
0013 %
0014 % Copyright (C) 2016 Wiggins Lab
0015 % Written by Paul Wiggins.
0016 % University of Washington, 2016
0017 % This file is part of SuperSegger.
0018 %
0019 % SuperSegger is free software: you can redistribute it and/or modify
0020 % it under the terms of the GNU General Public License as published by
0021 % the Free Software Foundation, either version 3 of the License, or
0022 % (at your option) any later version.
0023 %
0024 % SuperSegger is distributed in the hope that it will be useful,
0025 % but WITHOUT ANY WARRANTY; without even the implied warranty of
0026 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
0027 % GNU General Public License for more details.
0028 %
0029 % You should have received a copy of the GNU General Public License
0030 % along with SuperSegger.  If not, see <http://www.gnu.org/licenses/>.
0031 
0032 im = double(im);
0033 
0034 im(isinf(im(:))) = nan;
0035 
0036 if exist( 'imin', 'var') && ~isempty(  imin )
0037     im_min = imin;
0038 else
0039     im_min = min(im(:));
0040 end
0041 
0042 if ~exist( 'imax', 'var') || isempty(imax)
0043     imax = max(im(:));
0044 end
0045 
0046 im_max = imax-im_min;
0047 
0048 % subtract min
0049 im = im - double(im_min);
0050 
0051 
0052    % autogain and normalization to uint8
0053 im = uint8(255*im/double(im_max));
0054 
0055 end

ag

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SOURCE CODE