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brl_tip_cell_update.m
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brl_tip_cell_update.m
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function varargout = brl_tip_cell_update(varargin)
% BRL_TIP_CELL_UPDATE MATLAB code for brl_tip_cell_update.fig
% © 2015 Allen Institute.
% This file is part of smartACT.
% smartACT 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. smartACT 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 smartACT.
% If not, see <http://www.gnu.org/licenses/>.
%
% This package is currently not maintained and no support is implied.
% Questions may be directed to Brian Long
% <brianl@alleninstitute.org> with 'smartACT' in the subject line.
%
%
% BRL_TIP_CELL_UPDATE, by itself, creates a new BRL_TIP_CELL_UPDATE or raises the existing
% singleton*.
%
% H = BRL_TIP_CELL_UPDATE returns the handle to a new BRL_TIP_CELL_UPDATE or the handle to
% the existing singleton*.
%
% BRL_TIP_CELL_UPDATE('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in BRL_TIP_CELL_UPDATE.M with the given input arguments.
%
% BRL_TIP_CELL_UPDATE('Property','Value',...) creates a new BRL_TIP_CELL_UPDATE or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before brl_tip_cell_update_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to brl_tip_cell_update_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help brl_tip_cell_update
% Last Modified by GUIDE v2.5 24-Nov-2014 10:03:40
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @brl_tip_cell_update_OpeningFcn, ...
'gui_OutputFcn', @brl_tip_cell_update_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before brl_tip_cell_update is made visible.
function brl_tip_cell_update_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to brl_tip_cell_update (see VARARGIN)
% Choose default command line output for brl_tip_cell_update
handles.output = hObject;
tipCellData.archiveMode = 0;
% get the handle to the smartACT gui
tipCellData.smartACTh = findobj('name','smartACT');
tipCellData.runBh = handles.collectTipCellSubstackB;
tipCellData.runfunctionh = @collectTipCellSubstackB_Callback;
tipCellData.importh = @importStack;
tipCellData.findTiph =@locateTipB_Callback;
tipCellData.findCellh = @locateCellB_Callback;
tipCellData.findTipB =handles.locateTipB;
tipCellData.findCellB = handles.locateCellB;
set(handles.figure1, 'UserData', tipCellData);
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes brl_tip_cell_update wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = brl_tip_cell_update_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in useLatestFullStackB.
function useLatestFullStackB_Callback(hObject, eventdata, handles)
% hObject handle to useLatestFullStackB (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% get path to some relevant image data
tipCellData = get(handles.figure1, 'UserData');
global spStackdata
spUdat = get(tipCellData.smartACTh,'UserData');
imPath = spStackdata.lastFullStackRaw
%
% import defined substack.
%
tipCellData.tiprows = fliplr(255-[115 180]);
tipCellData.tipcols = [10 90];
tipCellData.tipzs = [50 67]
argh = brl_tif_read(imPath, 2,2,tipCellData.tiprows ,tipCellData.tipcols,tipCellData.tipzs);
tipCellData.rawTipImage = argh;
tipCellData.normTipImage = tipCellData.rawTipImage-percentile(tipCellData.rawTipImage(:), .05);
tipCellData.normTipImage = tipCellData.normTipImage/percentile(tipCellData.normTipImage(:), get( handles.tipNormalization, 'value'));
tipCellData.normTipImage = 255*tipCellData.normTipImage;
tipCellData.segTipImage = tipCellData.normTipImage>get(handles.tipThreshold,'Value');
%
% import defined substack.
%
tipCellData.lastCellLocation = []
tipCellData.cellrows = fliplr(255-[115 180]);
tipCellData.cellcols = [90 110];
tipCellData.cellzs = [95 115];
argh = brl_tif_read(imPath, 1,2,tipCellData.cellrows ,tipCellData.cellcols, tipCellData.cellzs);
tipCellData.rawCellImage = argh;
tipCellData.normCellImage = tipCellData.rawCellImage-percentile(tipCellData.rawCellImage(:), .05);
tipCellData.normCellImage = tipCellData.normCellImage/percentile(tipCellData.normCellImage(:), get( handles.cellNormalization, 'value'));
tipCellData.normCellImage = 255*tipCellData.normCellImage;
set(handles.imageFileT,'String', imPath);
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
% --- Executes on button press in analyzeArchivedStackB.
function analyzeArchivedStackB_Callback(hObject, eventdata, handles)
% hObject handle to analyzeArchivedStackB (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
tipCellData = get(handles.figure1, 'UserData');
% give option to load a stack and enter tip coordinates.
tipCellData.archiveMode = 1
[imPath,dir] = uigetfile('*.tif');
%
% import defined substack.
%
% tip location
tipCellData.tipLocation = round([ 93 122 16]);
tipCellData.tiprows = [max(tipCellData.tipLocation(2)-20,1) ,tipCellData.tipLocation(2)+20] ;
tipCellData.tipcols = [max(tipCellData.tipLocation(1)-20,1),tipCellData.tipLocation(1)+20 ];
tipCellData.tipzs = [max(tipCellData.tipLocation(3)-20,1) , tipCellData.tipLocation(3)+20];
argh = brl_tif_read(fullfile(dir,imPath), 2,2,tipCellData.tiprows ,tipCellData.tipcols,tipCellData.tipzs);
tipCellData.rawTipImage = argh;
tipCellData.normTipImage = tipCellData.rawTipImage-percentile(tipCellData.rawTipImage(:), .05);
tipCellData.normTipImage = tipCellData.normTipImage/percentile(tipCellData.normTipImage(:), get( handles.tipNormalization, 'value'));
tipCellData.normTipImage = 255*tipCellData.normTipImage;
tipCellData.segTipImage = tipCellData.normTipImage>get(handles.tipThreshold,'Value');
%
% import defined substack.
%
tipCellData.lastCellLocation = round([ 128 122 26])
tipCellData.cellrows = [max(tipCellData.lastCellLocation(2)-20,1) tipCellData.lastCellLocation(2)+20];
tipCellData.cellcols = [max(tipCellData.lastCellLocation(1)-20,1) tipCellData.lastCellLocation(1)+20];
tipCellData.cellzs = [max(tipCellData.lastCellLocation(3)-10,1), tipCellData.lastCellLocation(3)+10];
argh = brl_tif_read(fullfile(dir,imPath), 1,2,tipCellData.cellrows ,tipCellData.cellcols, tipCellData.cellzs);
size(argh)
tipCellData.cellzs = tipCellData.cellzs(1):tipCellData.cellzs(2);
tipCellData.cellzs =[tipCellData.cellzs(1) tipCellData.cellzs(size(argh,3))]
tipCellData.rawCellImage = argh;
tipCellData.normCellImage = tipCellData.rawCellImage-percentile(tipCellData.rawCellImage(:), .05);
tipCellData.normCellImage = tipCellData.normCellImage/percentile(tipCellData.normCellImage(:), get( handles.cellNormalization, 'value'));
tipCellData.normCellImage = 255*tipCellData.normCellImage;
set(handles.imageFileT,'String', fullfile(dir,imPath));
tipCellData
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
% --- Executes on selection change in tipImageSelectorPM.
function tipImageSelectorPM_Callback(hObject, eventdata, handles)
% hObject handle to tipImageSelectorPM (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns tipImageSelectorPM contents as cell array
% contents{get(hObject,'Value')} returns selected item from tipImageSelectorPM
tipCellData = get(handles.figure1, 'UserData');
if isfield(tipCellData,'tipLocation')
set(handles.tipReportedLocationT,'String', num2str(tipCellData.tipLocation([ 1 2 3]), '%.2f '))
end
currentSelection = get(hObject,'Value')
switch currentSelection
case 1
'image data'
imdat3D = tipCellData.rawTipImage;
mean(imdat3D(:))
axes(handles.axes1)
imagesc(squeeze(sum(imdat3D,3)));colormap gray
axes(handles.axes2)
imagesc((squeeze(sum(imdat3D,1)))');
axes(handles.axes3)
imagesc(squeeze(sum(imdat3D,2)));
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
case 2
'norm data'
imdat3D = tipCellData.normTipImage;
mean(imdat3D(:))
axes(handles.axes1)
imagesc(tipCellData.tipcols, tipCellData.tiprows,squeeze(sum(imdat3D,3)));
axes(handles.axes2)
imagesc((squeeze(sum(imdat3D,1)))');
axes(handles.axes3)
imagesc(squeeze(sum(imdat3D,2)));
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
case 3
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
feval(@locateTipB_Callback, handles.locateTipB, [], guidata(handles.locateTipB))
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
% 'segment data'
% % generate MIPs after smoothing
% get(handles.tipThreshold,'Value')
% mean(tipCellData.normTipImage(:))
% [tipCellData.im3, tipCellData.im2, tipCellData.im1] = brl_MIP_segmentation(tipCellData.normTipImage, get(handles.tipThreshold,'Value'));
% % and extract coordinates:
% tipCellData.tipdata = brl_find_tip_2(tipCellData.im3, tipCellData.im2, tipCellData.im1)
% tipCellData.tipdataStackCoordinates = brl_tipdata_to_stack(tipCellData.tipdata, tipCellData.tiprows(1), tipCellData.tipcols(1), tipCellData.tipzs(1))
%
% axes(handles.axes1)
% imagesc(tipCellData.tipcols, tipCellData.tiprows,tipCellData.im3);
% hold all, plot(max(tipCellData.tipdataStackCoordinates.tipj3),mean(tipCellData.tipdataStackCoordinates.tipi3), 'om')
% plot(tipCellData.tipdataStackCoordinates.tipj3,tipCellData.tipdataStackCoordinates.tipi3,'.g')
% hold off
% axes(handles.axes2)
% imagesc(tipCellData.tipcols, tipCellData.tipzs,(tipCellData.im1'));
% hold all, plot(mean(tipCellData.tipdataStackCoordinates.tipi1),max(tipCellData.tipdataStackCoordinates.tipj1), 'om') ,
% plot(tipCellData.tipdataStackCoordinates.tipi1,tipCellData.tipdataStackCoordinates.tipj1,'.g')
% hold off
% axes(handles.axes3)
% imagesc(tipCellData.tipzs, tipCellData.tiprows,tipCellData.im2);
% hold all, plot(mean(tipCellData.tipdataStackCoordinates.tipj2),mean(tipCellData.tipdataStackCoordinates.tipi2), 'om'),
% plot(tipCellData.tipdataStackCoordinates.tipj2,tipCellData.tipdataStackCoordinates.tipi2,'.g')
% hold off
%
% actualTipPixels = tipCellData.tipdata.coordinates+[tipCellData.tiprows(1) tipCellData.tipcols(1) tipCellData.tipzs(1)] -[1 1 1] ;
% tipCellData.tipMeasuredLocation = actualTipPixels;
% set(handles.tipMeasuredLocationT,'String', [sprintf('%.2f', actualTipPixels(1)), ' ', sprintf('%.2f', actualTipPixels(2)),' ',sprintf('%.2f', actualTipPixels(3))])
%
case 4 % cloak the pipet
tipCellData.tipdata.rp2
tipCellData.tipdata.ind2
% the object I want is the one that includes the centroid of the MIP pipets
coordinates3D = [tipCellData.tipdata.rp2(tipCellData.tipdata.ind2).Centroid(2), tipCellData.tipdata.rp3(tipCellData.tipdata.ind3).Centroid(1), tipCellData.tipdata.rp2(tipCellData.tipdata.ind2).Centroid(1)]
parameters.coordinates3D= round(coordinates3D);
tipCellData.tipBinary= brl_identify_tip(tipCellData.normTipImage> 255*get(handles.tipThreshold, 'Value'),parameters);
tipCellData.cloakedTipImg = brl_cloak_object(tipCellData.normTipImage, tipCellData.tipBinary);
axes(handles.axes1)
imagesc(tipCellData.tipcols, tipCellData.tiprows,squeeze(sum(tipCellData.cloakedTipImg,3)));
hold all,
plot(max(tipCellData.tipdataStackCoordinates.tipj3),mean(tipCellData.tipdataStackCoordinates.tipi3), 'om')
plot(tipCellData.tipdataStackCoordinates.tipj3,tipCellData.tipdataStackCoordinates.tipi3,'.g'),hold off
axes(handles.axes2)
imagesc(tipCellData.tipcols, tipCellData.tipzs+udat.substackSliceStart, squeeze(sum(tipCellData.cloakedTipImg,1))');
hold all,
plot(mean(tipCellData.tipdataStackCoordinates.tipi1),max(tipCellData.tipdataStackCoordinates.tipj1), 'om') ,
plot(tipCellData.tipdataStackCoordinates.tipi1,tipCellData.tipdataStackCoordinates.tipj1,'.g')
hold off
axes(handles.axes3)
imagesc(tipCellData.tipzs+udat.substackSliceStart, tipCellData.tiprows,squeeze(sum(tipCellData.cloakedTipImg,2)));
hold all, plot(mean(tipCellData.tipdataStackCoordinates.tipj2),mean(tipCellData.tipdataStackCoordinates.tipi2), 'om'),
plot(tipCellData.tipdataStackCoordinates.tipj2,tipCellData.tipdataStackCoordinates.tipi2,'.g')
hold off
actualTipPixels = tipCellData.tipdata.coordinates+[tipCellData.tiprows(1) tipCellData.tipcols(1) tipCellData.tipzs(1)] -[1 1 1] ;
tipCellData.tipMeasuredLocation = actualTipPixels;
set(handles.tipMeasuredLocationT,'String', [sprintf('%.2f', actualTipPixels(1)), ' ', sprintf('%.2f', actualTipPixels(2)),' ',sprintf('%.2f', actualTipPixels(3))])
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
end
% --- Executes on selection change in cellImageSelectorPM.
function cellImageSelectorPM_Callback(hObject, eventdata, handles)
% hObject handle to cellImageSelectorPM (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns cellImageSelectorPM contents as cell array
% contents{get(hObject,'Value')} returns selected item from cellImageSelectorPM
tipCellData = get(handles.figure1, 'UserData');
if isfield(tipCellData, 'lastCellLocation')
set(handles.cellOriginalLocationT,'String', num2str(tipCellData.lastCellLocation([2 1 3]) ,'%.2f '))
end
udat = get(findobj(0,'name','smartACT'),'UserData')
currentSelection = get(hObject,'Value')
switch currentSelection
case 1
'image data'
imdat3D = tipCellData.rawCellImage;
mean(imdat3D(:))
axes(handles.axes4)
imagesc(squeeze(sum(imdat3D,3)));colormap gray
axes(handles.axes5)
imagesc((squeeze(sum(imdat3D,1)))');
axes(handles.axes6)
imagesc(squeeze(sum(imdat3D,2)));
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
case 2
'norm data'
imdat3D = tipCellData.normCellImage;
mean(imdat3D(:))
axes(handles.axes4)
imagesc(tipCellData.cellcols, tipCellData.cellrows,squeeze(sum(imdat3D,3)));
axes(handles.axes5)
imagesc(tipCellData.cellcols, tipCellData.cellzs, (squeeze(sum(imdat3D,1)))');
axes(handles.axes6)
imagesc(tipCellData.cellzs, tipCellData.tiprows, squeeze(sum(imdat3D,2)));
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
imdat3D = tipCellData.normCellImage;
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
case 3
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
feval(@locateCellB_Callback, handles.locateCellB, [], guidata(handles.locateCellB))
guidata(hObject, handles);
% 'segment data';
% % generate MIPs after smoothing and locate cells
%
% mean(tipCellData.normTipImage(:))
% params.big = 20;
% params.small = 2;
% params.thresh =255*get(handles.cellThreshold,'Value');
% tipCellData.locateCellStruct = brl_locate_cells(tipCellData.normCellImage,params);
% keepRegions=[];
% actualCellPixels = [];
% for i = 1:numel(tipCellData.locateCellStruct.rpdata)
% idat= tipCellData.locateCellStruct.rpdata(i);
%
% actualCellPixels(i,:) = tipCellData.locateCellStruct.rpdata(i).Centroid([2 1 3])+[tipCellData.cellrows(1) tipCellData.cellcols(1) tipCellData.cellzs(1)+udat.substackSliceStart] -[1 1 1]
% if idat.Area >100
%
% keepRegions =[keepRegions; i]
% end
%
% end
%
%
% % figure out which object is the cell of interest
%
% % 1. find the objects that are big enough to be cells
%
% if numel(keepRegions)==1
% tipCellData.cellLocationPixels = actualCellPixels(keepRegions,:);
% cellnumber=1
%
%
% else
%
% % if there is more than one of these,
% % 2. find the object whos centroid is closest to the original cell location
%
% distances = sqrt(sum((actualCellPixels(keepRegions(:),:)- repmat(tipCellData.lastCellLocation([2,1,3]), numel(keepRegions),1)).^2,2));
%
% % note that this is NOT scaled to microns, just in voxels.
%
% if min(distances)> 15 % hard coded estimate here... many ways to parameterize this if needed
% set(handles.cellMeasuredLocationT,'String','cell displacement greater than ~18 microns')
% set(handles.figure1, 'UserData', tipCellData);
% guidata(hObject, handles);
% return
% end
% % take the closest one...
% cellnumber = keepRegions(distances(:)==min(distances(:)))
% tipCellData.cellLocationPixels = actualCellPixels(cellnumber,:);
%
%
%
% end
%
% tipCellData.cellzs+udat.substackSliceStart
%
% axes(handles.axes4)
% imagesc(tipCellData.cellcols, tipCellData.cellrows,squeeze(max(tipCellData.locateCellStruct.labelmatrix,[],3)));
% hold all, plot(actualCellPixels(:,2),actualCellPixels(:,1),'.b')
% plot(actualCellPixels(cellnumber,2),actualCellPixels(cellnumber,1),'or')
% hold off
% axes(handles.axes5)
% imagesc(tipCellData.cellcols, tipCellData.cellzs+udat.substackSliceStart,squeeze(max(tipCellData.locateCellStruct.labelmatrix,[],1))');
% hold all,plot(actualCellPixels(:,2),actualCellPixels(:,3),'.b')
% plot(actualCellPixels(cellnumber,2),actualCellPixels(cellnumber,3),'or')
% hold off
% axes(handles.axes6)
% imagesc(tipCellData.cellzs+udat.substackSliceStart,tipCellData.cellrows, squeeze(max(tipCellData.locateCellStruct.labelmatrix,[],2)));
% hold all, plot(actualCellPixels(:,3),actualCellPixels(:,1),'.b')
% plot(actualCellPixels(cellnumber,3),actualCellPixels(cellnumber,1),'or')
% hold off
%
%
% set(handles.cellMeasuredLocationT,'String', [sprintf('%.2f', actualCellPixels(cellnumber,1)), ' ', sprintf('%.2f', actualCellPixels(cellnumber,2)),' ',sprintf('%.2f', actualCellPixels(cellnumber,3))])
%
case 4 % cloak the pipet
% tipCellData.tipdata.rp2
% tipCellData.tipdata.ind2
%
% % the object I want is the one that includes the centroid of the MIP pipets
% coordinates3D = [tipCellData.tipdata.rp2(tipCellData.tipdata.ind2).Centroid(2), tipCellData.tipdata.rp3(tipCellData.tipdata.ind3).Centroid(1), tipCellData.tipdata.rp2(tipCellData.tipdata.ind2).Centroid(1)]
% parameters.coordinates3D= round(coordinates3D);
%
%
% tipCellData.tipBinary= brl_identify_tip(tipCellData.normTipImage> 255*get(handles.tipThreshold, 'Value'),parameters);
% tipCellData.cloakedTipImg = brl_cloak_object(tipCellData.normTipImage, tipCellData.tipBinary);
%
%
%
% axes(handles.axes1)
% imagesc(tipCellData.tipcols, tipCellData.tiprows,squeeze(sum(tipCellData.cloakedTipImg,3)));
% hold all, plot(max(tipCellData.tipdataStackCoordinates.tipj3),mean(tipCellData.tipdataStackCoordinates.tipi3), 'om'), plot(tipCellData.tipdataStackCoordinates.tipj3,tipCellData.tipdataStackCoordinates.tipi3,'.g')
% hold off
% axes(handles.axes2)
% imagesc(squeeze(sum(tipCellData.cloakedTipImg,1))');
% hold all, plot(mean(tipCellData.tipdataStackCoordinates.tipi1),max(tipCellData.tipdataStackCoordinates.tipj1), 'om') , plot(tipCellData.tipdataStackCoordinates.tipi1,tipCellData.tipdataStackCoordinates.tipj1,'.g')
% hold off
% axes(handles.axes3)
% imagesc(squeeze(sum(tipCellData.cloakedTipImg,2)));
% hold all, plot(mean(tipCellData.tipdataStackCoordinates.tipj2),mean(tipCellData.tipdataStackCoordinates.tipi2), 'om'), plot(tipCellData.tipdataStackCoordinates.tipj2,tipCellData.tipdataStackCoordinates.tipi2,'.g')
% hold off
%
% actualTipPixels = tipCellData.tipdata.coordinates+[tipCellData.tiprows(1) tipCellData.tipcols(1) tipCellData.tipzs(1)] -[1 1 1] ;
% tipCellData.tipMeasuredLocation = actualTipPixels;
% set(handles.tipMeasuredLocationT,'String', [sprintf('%.2f', actualTipPixels(1)), ' ', sprintf('%.2f', actualTipPixels(2)),' ',sprintf('%.2f', actualTipPixels(3))])
%
end
% --- Executes on button press in collectTipCellSubstackB.
function collectTipCellSubstackB_Callback(hObject, eventdata, handles)
% hObject handle to collectTipCellSubstackB (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% This will start the process of collecting a substack
global spStackdata
udat = get(findobj(0,'name','smartACT'),'UserData')
info.si = 'not used';
info.useLastFullStack = 1
% Collect a stack with both tip and cell.
%
% This requires first:
% 1.establishing a new set of fields for latest tip and cell locations in image and manipulator coordinates
% 2.at the same time, figure out how to log ALL of the relevant approach data in one place, including the 'trajectory' of
% % measured tip locations and measured cell locations, relevant files, etc.
% 3. then I need to use brl_tif_read to read in the correct subvolumes with the correct channel
%
zTopBuffer = 15; % increased from 10, 12/9/14
zBottomBuffer = 15; %increased form 10 12/15/14
imageZCoordinate = [max(udat.currentTipImage(3)-zTopBuffer,1) udat.currentCellImage(3)+zBottomBuffer]
startz = spStackdata.origStartRelZ+(spStackdata.zStepSize*(imageZCoordinate(1)-1));
stopz = spStackdata.origStartRelZ+(spStackdata.zStepSize*(imageZCoordinate(2)-2)) ; % note that we don't include slice at z+zdepth
% because we want the stack to be zdepth slices
spStackdata.substackGrab = 1;
spStackdata.ignorePostProcessing = 0;
udat.substackSliceStart =round(imageZCoordinate(1));
udat.substackSliceEnd = round(imageZCoordinate(2));
udat.substackStartz = startz;
udat.substackStopz = stopz;
set(findobj(0,'name','smartACT'),'UserData', udat)
set(handles.okCollectStackB,'enable', 'on', 'string', '<html>OK collect<br>Tip And Cell Stack')
set(handles.cancelB,'enable', 'on')
% now print the coordinates to the GUI to allow the user to check:
set(hObject,'string',[ 'start z = ', num2str(udat.substackStartz), ' stop z = ', num2str(udat.substackStopz)], 'fontsize', 8);
%
% try
% brl_collect_SI_Stack(startz, stopz)
% catch
% set(findobj(0,'name','smartACT'),'UserData', udat)
% end
% the rest of the action will take place triggered by the OK button
udat.substackToCollect = 'tipAndCell';
set(findobj(0,'name','smartACT'),'UserData', udat)
%importstack()
guidata(hObject, handles);
% --- Executes on button press in okCollectStackB.
function okCollectStackB_Callback(hObject, eventdata, handles)
% hObject handle to okCollectStackB (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
udat = get(findobj(0,'name','smartACT'),'UserData')
set(handles.okCollectStackB,'enable', 'off')
set(handles.cancelB,'enable', 'off')
switch udat.substackToCollect
case 'tipAndCell'
brl_collect_SI_Stack(udat.substackStartz, udat.substackStopz)
case 'cellOnly'
brl_collect_SI_Stack(udat.cellSubstackStartz, udat.cellSubstackStopz)
end
set(findobj(0,'name','smartACT'),'UserData', udat)
% the rest of the action will take place inside brl_sp_grab_handler, but
% use the other buttons here via feval
set(handles.collectTipCellSubstackB,'string','<html>Calculate New <br> Tip and Cell Substack');
set(handles.collectCellSubstackB,'string','<html>Calculate New <br> Cell Substack');
guidata(hObject, handles);
% --- Executes on button press in cancelB.
function cancelB_Callback(hObject, eventdata, handles)
% hObject handle to cancelB (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
set(handles.okCollectStackB,'enable', 'off')
set(handles.cancelB,'enable', 'off')
set(handles.collectTipCellSubstackB,'string','<html>Calculate New <br> Tip and Cell Substack');
set(handles.collectCellSubstackB,'string','<html>Calculate New <br> Cell Substack');
guidata(hObject, handles);
% --- internal function to handle reading in an existing file .
function importStack(~)
% hObject handle to anything ? (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
tcuh = findobj('name','brl_tip_cell_update');
tipCellData = get(tcuh, 'UserData');
global spStackdata
if spStackdata.acquisitionRunning ==1
return
end
udat = get(findobj(0,'Name', 'smartACT'), 'UserData');
if numel(udat) ==0
return
end
tipCellData.archiveMode = 0;
%
tipCellData.file = brl_get_latest_file(udat.directory, '*.tif', 'Norm')
% this will be the last .tif file created, which should be the substack.
% there's not too much information to indicate this... I can check the last
scimdata = scim_openTif(tipCellData.file);
scimdata.acq
if udat.substackSliceEnd - udat.substackSliceStart + 1 == scimdata.acq.numberOfZSlices
'imported image is substack'
end
%tipCellData.file='E:\Data\BRLtest\tx\Cux2B002.tif'
%
% import defined substack.
%
% tip location
tipCellData.tipLocation = udat.currentTipImage([1 2 3])
tipCellData.tipSubstackLocation = [tipCellData.tipLocation]-[0 0 udat.substackSliceStart-1]
tipCellData.tiprows = round([max(tipCellData.tipSubstackLocation(1)-20,1) ,tipCellData.tipSubstackLocation(1)+20]) ;
tipCellData.tipcols = round([max(tipCellData.tipSubstackLocation(2)-20,1),tipCellData.tipSubstackLocation(2)+20 ]);
tipCellData.tipzs = round([max(tipCellData.tipSubstackLocation(3)-20,1) , tipCellData.tipSubstackLocation(3)+20]);
argh = brl_tif_read(tipCellData.file, get(udat.tipChannelh,'value'),2,tipCellData.tiprows ,tipCellData.tipcols,tipCellData.tipzs);
zlist = tipCellData.tipzs(1):tipCellData.tipzs(2);
tipCellData.tipzs =[zlist(1) zlist(size(argh,3))]
tipCellData.rawTipImage = argh;
tipCellData.normTipImage = tipCellData.rawTipImage-percentile(tipCellData.rawTipImage(:), .05);
tipCellData.normTipImage = tipCellData.normTipImage/percentile(tipCellData.normTipImage(:), get( findobj('tag','tipNormalization'), 'value'));
tipCellData.normTipImage = 255*tipCellData.normTipImage;
tipCellData.segTipImage = tipCellData.normTipImage>get(findobj('tag','tipThreshold'),'Value');
%
% import defined substack.
%
tipCellData.lastCellLocation = udat.currentCellImage([2 1 3]);
tipCellData.cellSubstackLocation = tipCellData.lastCellLocation-[0 0 udat.substackSliceStart-1]
tipCellData.cellrows = round([max(tipCellData.cellSubstackLocation(1)-20,1) tipCellData.cellSubstackLocation(1)+20]);
tipCellData.cellcols = round([max(tipCellData.cellSubstackLocation(2)-20,1) tipCellData.cellSubstackLocation(2)+20]);
tipCellData.cellzs = round([max(tipCellData.cellSubstackLocation(3)-10,1), tipCellData.cellSubstackLocation(3)+10])
argh = brl_tif_read(tipCellData.file, get(udat.cellChannelh,'value'),2,tipCellData.cellrows ,tipCellData.cellcols, tipCellData.cellzs);
size(argh)
zlist = tipCellData.cellzs(1):tipCellData.cellzs(2);
tipCellData.cellzs =[zlist(1) zlist(size(argh,3))]
tipCellData.rawCellImage = argh;
tipCellData.normCellImage = tipCellData.rawCellImage-percentile(tipCellData.rawCellImage(:), .05);
tipCellData.normCellImage = tipCellData.normCellImage/percentile(tipCellData.normCellImage(:), get( findobj('tag','cellNormalization'), 'value'));
tipCellData.normCellImage = 255*tipCellData.normCellImage;
set(findobj('tag', 'imageFileT'),'String', tipCellData.file);
set(findobj(0,'Name', 'smartACT'), 'UserData', udat);
set(tcuh, 'UserData', tipCellData);
% --- Executes on button press in locateTipB.
function locateTipB_Callback(hObject, eventdata, handles)
% hObject handle to locateTipB (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
udat = get(findobj('name', 'smartACT'), 'userdata');
% recapitulate what's in the popup menu callbacks- this callback will be
% called externally
%
% feval(get(handles.tipNormalization,'Callback'), handles.tipNormalization, [])
% feval(get(handles.tipThreshold,'Callback'), handles.tipThreshold, [])
tipCellData = get(handles.figure1, 'UserData')
set(handles.tipReportedLocationT,'String', num2str(tipCellData.tipLocation([1 2 3]), '%.2f '))
% generate MIPs after smoothing
tval = get(handles.tipThreshold,'Value');
mean(tipCellData.normTipImage(:))
tipCellData.normTipImage = tipCellData.rawTipImage-percentile(tipCellData.rawTipImage(:), .05);
tipCellData.normTipImage(tipCellData.normTipImage(:)<0)=0;
tipCellData.normTipImage = tipCellData.normTipImage/percentile(tipCellData.normTipImage(:), get( handles.tipNormalization, 'value'));
tipCellData.normTipImage(tipCellData.normTipImage(:)>1)=1;
tipCellData.normTipImage = 255*tipCellData.normTipImage;
[tipCellData.im3, tipCellData.im2, tipCellData.im1] = brl_MIP_segmentation(tipCellData.normTipImage, tval);
% and extract coordinates:
tipCellData.tipdata = brl_find_tip_2(tipCellData.im3, tipCellData.im2, tipCellData.im1)
testStruct = tipCellData.tipdata
tipCellData.tipdataStackCoordinates = brl_tipdata_to_stack(tipCellData.tipdata, tipCellData.tiprows(1), tipCellData.tipcols(1), tipCellData.tipzs(1))
axes(handles.axes1)
imagesc(tipCellData.tipcols, tipCellData.tiprows,tipCellData.im3);
hold all, plot(max(tipCellData.tipdataStackCoordinates.tipj3),mean(tipCellData.tipdataStackCoordinates.tipi3), 'om'), plot(tipCellData.tipdataStackCoordinates.tipj3,tipCellData.tipdataStackCoordinates.tipi3,'.g')
hold off
axes(handles.axes2)
imagesc(tipCellData.tipcols, tipCellData.tipzs,(tipCellData.im1'));
hold all, plot(mean(tipCellData.tipdataStackCoordinates.tipi1),max(tipCellData.tipdataStackCoordinates.tipj1), 'om') , plot(tipCellData.tipdataStackCoordinates.tipi1,tipCellData.tipdataStackCoordinates.tipj1,'.g')
hold off
axes(handles.axes3)
imagesc(tipCellData.tipzs, tipCellData.tiprows,tipCellData.im2);
hold all, plot(mean(tipCellData.tipdataStackCoordinates.tipj2),mean(tipCellData.tipdataStackCoordinates.tipi2), 'om'), plot(tipCellData.tipdataStackCoordinates.tipj2,tipCellData.tipdataStackCoordinates.tipi2,'.g')
hold off
actualTipPixels = tipCellData.tipdata.coordinates+[tipCellData.tiprows(1) tipCellData.tipcols(1) tipCellData.tipzs(1)+udat.substackSliceStart] -[1 1 1] ;
tipCellData.tipMeasuredLocation = actualTipPixels;
set(handles.tipMeasuredLocationT,'String', [sprintf('%.2f', actualTipPixels(1)), ' ', sprintf('%.2f', actualTipPixels(2)),' ',sprintf('%.2f', actualTipPixels(3))])
% now update the smartACT userdata struct with the new tip coordinates
iTip = udat.Locations.pipetTip;
% and in microns
actualTipMicrons= actualTipPixels([2 1 3]).*([udat.xScale udat.yScale udat.zScale]);
% and relative coordinates for the MP285
actualTipMP285= [iTip(1:2) -iTip(3)]+[-actualTipMicrons(1:2) actualTipMicrons(3)];
if ~isfield(udat, 'tipTraj')
udat.tipTraj=[];
end
% update a trajectory for the tip. it's ok if the last position
% repeats or something.... | prev tip pixels | prev tip Microns | prev tip mp285 | new tip pixels | new tip microns | new tip mp285
udat.tipTraj = [udat.tipTraj; [udat.currentTipImage, udat.currentTipMicrons, udat.CurrentLocation,actualTipPixels, actualTipMicrons, actualTipMP285]];
newt = udat.tipTraj ; % just to echo to command line for debugging
udat.potentialCoordinates.actualTipPixels = actualTipPixels;
udat.potentialCoordinates.actualTipMicrons = actualTipMicrons;
udat.potentialCoordinates.actualTipMP285 = actualTipMP285;
udat.potentialCoordinates.tipThreshold = get(handles.tipThreshold, 'value');
udat.potentialCoordinates.tipNorm = get(handles.tipNormalization,'value');
udat.tipUpdateWorked = 1;
set(findobj('name', 'smartACT'), 'userdata',udat);
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
% --- Executes on button press in locateCellB.
function locateCellB_Callback(hObject, eventdata, handles)
% hObject handle to locateCellB (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% feval(get(handles.cellNormalization,'Callback'), handles.cellNormalization, [])
% feval(get(handles.cellThreshold,'Callback'), handles.cellThreshold, [])
udat = get(findobj('name', 'smartACT'), 'userdata');
tipCellData = get(handles.figure1, 'UserData');
set(handles.cellOriginalLocationT,'String', num2str(tipCellData.lastCellLocation([1 2 3]) ,'%.2f '))
params.big = 20;
params.small = 2;
params.thresh =255*get(handles.cellThreshold,'Value');
tipCellData.locateCellStruct = brl_locate_cells(tipCellData.normCellImage,params);
keepRegions=[];
actualCellPixels = [];
for i = 1:numel(tipCellData.locateCellStruct.rpdata)
idat= tipCellData.locateCellStruct.rpdata(i);
actualCellPixels(i,:) = tipCellData.locateCellStruct.rpdata(i).Centroid([2 1 3])+[tipCellData.cellrows(1) tipCellData.cellcols(1) tipCellData.cellzs(1)+udat.substackSliceStart] -[1 1 1]
if idat.Area > 100
keepRegions =[keepRegions; i]
end
end
% figure out which object is the cell of interest
% 1. find the objects that are big enough to be cells
distances = sqrt(sum((actualCellPixels(keepRegions(:),:)- repmat(tipCellData.lastCellLocation([1 2 3]), numel(keepRegions),1)).^2,2))
if numel(keepRegions)==1
tipCellData.cellLocationPixels = actualCellPixels(keepRegions,:);
cellnumber =1;
elseif numel(keepRegions)==0
udat.cellUpdateWorked = 0;
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
else
% if there is more than one of these,
% 2. find the object whos centroid is closest to the original cell location
distances = sqrt(sum((actualCellPixels(keepRegions(:),:)- repmat(tipCellData.lastCellLocation([1 2 3]), numel(keepRegions),1)).^2,2))
% note that this is NOT scaled to microns, just in voxels.
if min(distances)> 17 % hard coded estimate here... many ways to parameterize this if needed
set(handles.cellMeasuredLocationT,'String','cell displacement greater than ~20 microns')
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
return
end
% take the closest one...
cellnumber = keepRegions(distances(:)==min(distances(:)));
tipCellData.cellLocationPixels = actualCellPixels(cellnumber,:);
end
axes(handles.axes4)
imagesc(tipCellData.cellcols, tipCellData.cellrows,squeeze(max(tipCellData.locateCellStruct.labelmatrix,[],3)));
hold all, plot(actualCellPixels(:,2),actualCellPixels(:,1),'.b')
plot(actualCellPixels(cellnumber,2),actualCellPixels(cellnumber,1),'or')
hold off
axes(handles.axes5)
imagesc(tipCellData.cellcols, tipCellData.cellzs+udat.substackSliceStart,squeeze(max(tipCellData.locateCellStruct.labelmatrix,[],1))');
hold all,plot(actualCellPixels(:,2),actualCellPixels(:,3),'.b')
plot(actualCellPixels(cellnumber,2),actualCellPixels(cellnumber,3),'or')
hold off
axes(handles.axes6)
imagesc(tipCellData.cellzs+udat.substackSliceStart,tipCellData.cellrows, squeeze(max(tipCellData.locateCellStruct.labelmatrix,[],2)));
hold all, plot(actualCellPixels(:,3),actualCellPixels(:,1),'.b')
plot(actualCellPixels(cellnumber,3),actualCellPixels(cellnumber,1),'or')
hold off
set(handles.cellMeasuredLocationT,'String', [sprintf('%.2f', actualCellPixels(cellnumber,1)), ' ', sprintf('%.2f', actualCellPixels(cellnumber,2)),' ',sprintf('%.2f', actualCellPixels(cellnumber,3))])
% now update the smartACT userdata struct with the new cell coordinates
iTip = udat.Locations.pipetTip
% convert from pixels to microns
aCellMicrons= actualCellPixels(cellnumber,:).*([udat.xScale udat.yScale udat.zScale])
iTip
actualCellMicrons = aCellMicrons
% and substract iTip location to get to relative coordinates for the MP285
actualCellMP285= actualCellMicrons-iTip([2 1 3])
actualCellMP285 = [actualCellMP285([2 1]) actualCellMP285( 3)]
udat.currentCellMP285= [iTip(1:2) -iTip(3)]+[-udat.currentCellMicrons(1:2) udat.currentCellMicrons(3)];
udat.cellTraj=[]
if ~isfield(udat, 'cellTraj')
udat.cellTraj=[];
end
% udat
% actualCellPixels
% actualCellMicrons
% actualCellMP285
% this coordinate transformation is a wreck. image locations are good:
% udat.currentCellImage, vs actualCellPixels(cellnumber,[2 1 3]), and
% these are used later
udat.cellTraj = [udat.cellTraj; [udat.currentCellImage,actualCellPixels(cellnumber,[2 1 3])]];
newt = udat.cellTraj % just to echo to command line for debugging
udat.potentialCoordinates.currentCellImage = actualCellPixels(cellnumber,[2 1 3]);
udat.potentialCoordinates.cellThreshold = get(handles.cellThreshold, 'value');
udat.potentialCoordinates.cellNorm = get(handles.cellNormalization,'value');
udat.cellUpdateWorked = 1;
set(findobj('name', 'smartACT'), 'userdata',udat);
set(handles.figure1, 'UserData', tipCellData);
guidata(hObject, handles);
% --- Executes on slider movement.
function cellThreshold_Callback(hObject, eventdata, handles)
% hObject handle to cellThreshold (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
tipCellData = get(handles.figure1, 'UserData');
set(handles.cellThreshValT,'String', num2str(get(handles.cellThreshold,'value')));
tipCellData.segCellImage = tipCellData.normCellImage>255*get(handles.cellThreshold,'Value');
set(handles.cellThreshValT,'String', num2str(get(handles.cellThreshold,'value')));
set(handles.figure1, 'UserData', tipCellData);
feval( @cellImageSelectorPM_Callback,handles.cellImageSelectorPM,[], handles)
guidata(hObject, handles);
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
% --- Executes on slider movement.
function cellNormalization_Callback(hObject, eventdata, handles)
% hObject handle to cellNormalization (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
tipCellData = get(handles.figure1, 'UserData');
tipCellData.normCellImage = tipCellData.rawCellImage-percentile(tipCellData.rawCellImage(:), .05);
tipCellData.normCellImage(tipCellData.normCellImage(:)<0)=0;
tipCellData.normCellImage = tipCellData.normCellImage/percentile(tipCellData.normCellImage(:), get( handles.cellNormalization, 'value'));
tipCellData.normTipImage(tipCellData.normTipImage(:)>1)=1;
tipCellData.normCellImage = 255*tipCellData.normCellImage;
set(handles.cellNormValT,'String', num2str(get(handles.cellNormalization,'value')));
feval( @cellImageSelectorPM_Callback, handles.cellImageSelectorPM, [], handles)