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registers2p.m
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registers2p.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% RegisterS2P %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Semi-automatic cross-day ROI registration for calcium imaging data
% processed through Suite2P (written by Marius Pachitariu). For more
% information see readme.
%
% Written by Henry Dalgleish 2017.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function varargout = registers2p(varargin)
% REGISTERS2P MATLAB code for registers2p.fig
% REGISTERS2P, by itself, creates a new REGISTERS2P or raises the existing
% singleton*.
%
% H = REGISTERS2P returns the handle to a new REGISTERS2P or the handle to
% the existing singleton*.
%
% REGISTERS2P('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in REGISTERS2P.M with the given input arguments.
%
% REGISTERS2P('Property','Value',...) creates a new REGISTERS2P or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before registers2p_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to registers2p_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 registers2p
% Last Modified by GUIDE v2.5 09-Aug-2017 16:56:55
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @registers2p_OpeningFcn, ...
'gui_OutputFcn', @registers2p_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 registers2p is made visible.
function registers2p_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 registers2p (see VARARGIN)
% Choose default command line output for registers2p
handles.output = hObject;
addlistener(handles.contrast_slider,'ContinuousValueChange',@(hObject, event) adjust_contrast(hObject, event));
num_ims = 2;
handles.image_display = [];
handles.roi_display = [];
handles.cursors(1).scatter = [];
handles.cursors(2).scatter = [];
handles.targets(1).scatter = [];
handles.targets(2).scatter = [];
handles.dil_targets_handles = [];
handles.original_targets = [];
handles.plotted_targets = [];
handles.overlay = false;
handles.im_flag = true;
handles.colors = [0 0 0];
handles.target_sizes = [15 70];
handles.bg_color = [1 1 1 ; 0 1 0];
handles.mask_fields = fields(handles);
handles.mask_fields = handles.mask_fields(cellfun(@(y) ~isempty(strfind(y,'mask_text')),handles.mask_fields));
handles.mask_field_nums = cellfun(@(x) str2num(x(strfind(x,'text')+4:end)),handles.mask_fields);
for i = 1:num_ims
handles.files(i).filepath = [];
% Variables
handles.files(i).num_masks = 6;
handles.files(i).image{1} = zeros(512,512,handles.files(i).num_masks);
handles.files(i).image{2} = handles.files(i).image{1};
handles.files(i).dims = size(handles.files(i).image{1});
handles.files(i).dims = handles.files(i).dims(1:2);
handles.files(i).rois_ibar = [];
handles.files(i).centroids = [];
handles.files(i).iscell_idcs = [];
% Calculated
handles.files(i).roi_status = [];
handles.files(i).roi_idcs = [];
handles.files(i).num_rois = [];
handles.files(i).roi_areas = [];
handles.files(i).iscell = [];
handles.files(i).loaded = false;
handles.files(i).targets_overlap_yx = [nan nan];
% Defaults
handles.files(i).default_image = handles.files(i).image;
handles.files(i).default_dims = [];
handles.files(i).default_rois_ibar = [];
handles.files(i).default_centroids = [];
handles.files(i).default_roi_idcs = [];
handles.files(i).default_roi_areas = [];
handles.files(i).num_rois = [];
end
handles.overlap_thold = 0.6;
handles.targets_overlap_thold = 5;
handles = set_gui_defaults(hObject,handles);
handles.transform_filepath = [];
handles.tform = [];
handles.tform_direction = [0 1];
handles.transform_loaded = false;
handles.targets_filepath = [];
handles.targets_image = [];
handles.dil_targets_yx = [];
handles.tformed_targets_yx = [nan nan];
handles.tformed_targets_default = [nan nan];
handles.targets_loaded = false;
handles.targets_s2p_rois = [];
handles.selected_targets = false;
handles.targets_overlapped = false;
handles.displayed_image = 1;
handles.displayed_mask = 1;
handles.proc_flag = 1;
handles.image_display = imagesc(handles.image_axis,handles.files(1).image{1}(:,:,1),'ButtonDownFcn',@lasso_targets);
colormap(handles.image_axis,'gray')
axis(handles.image_axis,'square','off')
hold(handles.image_axis,'on');
handles.image_axis.Units = 'normalized';
handles.targets(1).scatter = scatter(handles.image_axis,[],[],30,'r.');
handles.targets(2).scatter = scatter(handles.image_axis,[],[],30,'r.');
handles.original_targets = scatter(handles.image_axis,[],[],20,[0.6 0.6 0.6],'o');
handles.plotted_targets = scatter(handles.image_axis,[],[],handles.target_sizes(1),[1 0 1],'o','filled');
handles.cursors(1).scatter = scatter(handles.image_axis,nan,nan,50,'o','MarkerFaceColor',[0 0.5 1],'MarkerEdgeColor',[0 0.5 1]);
handles.roi_display = image(handles.roi_axis,handles.files(1).image{1}(:,:,1),'ButtonDownFcn',@select_rois);
colormap(handles.roi_axis,'gray')
axis(handles.roi_axis,'square','off')
hold(handles.roi_axis,'on');
handles.image_axis.Units = 'normalized';
handles.cursors(2).scatter = scatter(handles.roi_axis,nan,nan,50,'o','MarkerFaceColor',[0 0.5 1],'MarkerEdgeColor',[0 0.5 1]);
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes registers2p wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = registers2p_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;
function fixed_textbox_Callback(hObject, eventdata, handles)
% hObject handle to fixed_textbox (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,'String') returns contents of fixed_textbox as text
% str2double(get(hObject,'String')) returns contents of fixed_textbox as a double
% --- Executes during object creation, after setting all properties.
function fixed_textbox_CreateFcn(hObject, eventdata, handles)
% hObject handle to fixed_textbox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function transform_textbox_Callback(hObject, eventdata, handles)
% hObject handle to transform_textbox (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,'String') returns contents of transform_textbox as text
% str2double(get(hObject,'String')) returns contents of transform_textbox as a double
% --- Executes during object creation, after setting all properties.
function transform_textbox_CreateFcn(hObject, eventdata, handles)
% hObject handle to transform_textbox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function moving_textbox_Callback(hObject, eventdata, handles)
% hObject handle to moving_textbox (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,'String') returns contents of moving_textbox as text
% str2double(get(hObject,'String')) returns contents of moving_textbox as a double
% --- Executes during object creation, after setting all properties.
function moving_textbox_CreateFcn(hObject, eventdata, handles)
% hObject handle to moving_textbox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in load_fixed_button.
function load_fixed_button_Callback(hObject, eventdata, handles)
% hObject handle to load_fixed_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
idx = 1;
handles = load_s2p_struct(hObject,handles,idx);
guidata(hObject,handles)
% --- Executes on button press in load_moving_button.
function load_moving_button_Callback(hObject, eventdata, handles)
% hObject handle to load_moving_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
idx = 2;
handles = load_s2p_struct(hObject,handles,idx);
guidata(hObject,handles)
% --- Executes on button press in load_transform_button.
function load_transform_button_Callback(hObject, eventdata, handles)
% hObject handle to load_transform_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if ~isempty(handles.files(1).filepath) && ~isempty(handles.files(2).filepath)
name_idcs = find(cellfun(@(x) ~isempty(x),{handles.files(:).filepath}));
dd = fileparts(handles.files(name_idcs(1)).filepath);
try
[f,d] = uigetfile([dd filesep '*.mat']);
catch
[f,d] = uigetfile('*.mat');
end
if f~=0
handles.transform_filepath = [d filesep f];
handles.transform_textbox.String = handles.transform_filepath;
load(handles.transform_filepath)
handles.tform = t.tform;
handles.tform_direction = t.tform_direction;
handles.transform_loaded = true;
order = handles.tform_direction+1;
handles = set_gui_defaults(hObject,handles);
handles = reload_roi_defaults(handles);
i = 0;
h = waitbar(i,'Fitting transform...');
steps = (handles.files(order(2)).num_masks * 2) + 3;
i = i+1;
waitbar(i / steps,h,'Registering images...')
for p = 1:2
for m = 1:handles.files(order(2)).num_masks
handles.files(order(2)).image{p}(:,:,m) = imwarp(handles.files(order(2)).image{p}(:,:,m),handles.tform,'OutputView',imref2d(size(handles.files(order(2)).image{1}(:,:,1))));
i = i+1;
waitbar(i / steps);
end
end
i = i+1;
waitbar(i / steps,h,'Registering ROIs...')
[handles] = transform_rois(handles,order(2));
if handles.targets_loaded && handles.targets_overlapped
handles = reset_targets_overlap(handles);
end
waitbar(1);
close(h);
update_displays(hObject,handles);
guidata(hObject,handles)
end
end
% --- Executes on button press in load_targets_button.
function load_targets_button_Callback(hObject, eventdata, handles)
% hObject handle to load_targets_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[f,d] = uigetfile('*.*');
if f~=0
handles.targets_filepath = [d f];
handles.targets_textbox.String = handles.targets_filepath;
[~,~,ext] = fileparts(handles.targets_filepath);
switch ext
case {'.tif' '.tiff'}
handles.targets_image = imread(handles.targets_filepath);
handles.tformed_targets_yx = [];
[handles.tformed_targets_yx(:,1),handles.tformed_targets_yx(:,2)] = find(handles.targets_image);
handles.tformed_targets_default = handles.tformed_targets_yx;
handles.targets_loaded = true;
handles.targets_s2p_rois = zeros(size(handles.tformed_targets_yx,1),3);
handles.colors = repmat([1 0 0],[size(handles.tformed_targets_yx(:,1)),1]);
handles.selected_targets = false * handles.tformed_targets_yx(:,1);
case {'.mat'}
load(handles.targets_filepath)
if size(params.targets_yxzc,2) == 4
[~,order] = sort(params.targets_yxzc(:,4));
else
order = 1:size(params.targets_yxzc,1);
end
handles.tformed_targets_yx = params.targets_yxzc(order,1:2);
handles.tformed_targets_default = handles.tformed_targets_yx;
handles.targets_loaded = true;
handles.targets_s2p_rois = zeros(size(handles.tformed_targets_yx,1),3);
handles.colors = repmat([1 0 0],[size(handles.tformed_targets_yx(:,1)),1]);
handles.selected_targets = false * handles.tformed_targets_yx(:,1);
end
if handles.targets_loaded
if handles.targets_overlapped
handles = reset_targets_overlap(handles);
end
handles = plot_targets(hObject,handles);
end
end
guidata(hObject,handles)
% --- Executes on button press in save_tform_button.
function save_tform_button_Callback(hObject, eventdata, handles)
% hObject handle to save_tform_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if ~isempty(handles.files(1).filepath) && ~isempty(handles.files(2).filepath) && ~isempty(handles.tform)
name_idcs = find(cellfun(@(x) ~isempty(x),{handles.files(:).filepath}));
dd = fileparts(handles.files(name_idcs(1)).filepath);
name_idcs = find(cellfun(@(x) ~isempty(x),{handles.files(:).filepath}));
name_chunks = cell(1,numel(name_idcs));
ff = name_chunks;
for i = 1:numel(name_idcs)
[dd,ff{i}] = fileparts(handles.files(name_idcs(i)).filepath);
name_chunks{i} = ff{i}(3:end);
name_chunks{i} = strrep(name_chunks{i},'proc','');
end
default_name = [name_chunks{:}];
default_name(end) = [];
default_name = [default_name '_tform'];
[f,d] = uiputfile([dd filesep '*.mat'],'Save...',[dd filesep default_name '.mat']);
if d ~= 0
t.tform = handles.tform;
t.tform_direction = handles.tform_direction;
save([d filesep f],'t');
end
end
% --- Executes on button press in register_button.
function register_button_Callback(hObject, eventdata, handles)
% hObject handle to register_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if handles.files(1).loaded && handles.files(2).loaded
order = handles.tform_direction+1;
moving_im = double(handles.files(order(2)).default_image{handles.proc_flag}(:,:,handles.displayed_mask));
moving_lims = handles.files(order(2)).lims{handles.proc_flag}(handles.displayed_mask,:);
moving_im(moving_im>moving_lims(2)) = moving_lims(2);
moving_im(moving_im<moving_lims(1)) = moving_lims(1);
moving_im = moving_im-min(moving_im(:));
moving_im = moving_im ./ max(moving_im(:));
moving_im = uint8(moving_im*255);
static_im = double(handles.files(order(1)).default_image{handles.proc_flag}(:,:,handles.displayed_mask));
static_lims = handles.files(order(1)).lims{handles.proc_flag}(handles.displayed_mask,:);
static_im(static_im>static_lims(2)) = static_lims(2);
static_im(static_im<static_lims(1)) = static_lims(1);
static_im = static_im-min(static_im(:));
static_im = static_im ./ max(static_im(:));
static_im = uint8(static_im*255);
%moving_im = moving_im - min(moving_im(:));
%static_im = static_im - min(static_im(:));
%moving_im = uint8(moving_im/max(max(moving_im))*255);
%static_im = uint8(static_im/max(max(static_im))*255);
[movingPoints, fixedPoints] = cpselect(moving_im, static_im, 'wait',true);
if ~isempty(movingPoints) && ~isempty(fixedPoints)
i = 0;
h = waitbar(i,'Fitting transform...');
handles.tform = fitgeotrans(movingPoints, fixedPoints, 'affine');
handles = set_gui_defaults(hObject,handles);
handles = reload_roi_defaults(handles);
steps = (handles.files(order(2)).num_masks * 2) + 3;
i = i+1;
waitbar(i / steps,h,'Registering images...')
for p = 1:2
for m = 1:handles.files(order(2)).num_masks
handles.files(order(2)).image{p}(:,:,m) = imwarp(handles.files(order(2)).image{p}(:,:,m),handles.tform,'OutputView',imref2d(size(handles.files(order(2)).image{1}(:,:,1))));
i = i+1;
waitbar(i / steps);
end
end
i = i+1;
waitbar(i / steps,h,'Registering ROIs...')
handles = transform_rois(handles,order(2));
if handles.targets_loaded && handles.targets_overlapped
handles = reset_targets_overlap(handles);
end
update_displays(hObject,handles);
waitbar(1);
close(h);
end
end
guidata(hObject,handles);
% --- Executes on button press in reset_button.
function reset_button_Callback(hObject, eventdata, handles)
% hObject handle to reset_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = reload_roi_defaults(handles);
handles.transform_filepath = [];
handles.tform = [];
handles.tform_direction = [0 1];
handles.transform_loaded = false;
handles.transform_textbox.String = '...';
handles.tformed_targets_yx = handles.tformed_targets_default;
handles = reset_rois_overlap(handles);
if handles.targets_loaded && handles.targets_overlapped
handles = reset_targets_overlap(handles);
end
update_displays(hObject,handles);
guidata(hObject,handles);
function targets_textbox_Callback(hObject, eventdata, handles)
% hObject handle to targets_textbox (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,'String') returns contents of targets_textbox as text
% str2double(get(hObject,'String')) returns contents of targets_textbox as a double
% --- Executes during object creation, after setting all properties.
function targets_textbox_CreateFcn(hObject, eventdata, handles)
% hObject handle to targets_textbox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes during object creation, after setting all properties.
function image_axis_CreateFcn(hObject, eventdata, handles)
% hObject handle to image_axis (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: place code in OpeningFcn to populate image_axis
% --- Executes on mouse press over axes background.
function roi_axis_ButtonDownFcn(hObject, eventdata, handles)
% hObject handle to roi_axis (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes on mouse press over axes background.
function image_axis_ButtonDownFcn(hObject, eventdata, handles)
% hObject handle to image_axis (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes on button press in save_button.
function save_button_Callback(hObject, eventdata, handles)
% hObject handle to save_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if ~isempty(handles.files(1).filepath) || ~isempty(handles.files(2).filepath)
name_idcs = find(cellfun(@(x) ~isempty(x),{handles.files(:).filepath}));
name_chunks = cell(1,numel(name_idcs));
ff = name_chunks;
for i = 1:numel(name_idcs)
[dd,ff{i}] = fileparts(handles.files(name_idcs(i)).filepath);
name_chunks{i} = ff{i}(3:end);
name_chunks{i} = strrep(name_chunks{i},'proc','');
end
default_name = [name_chunks{:}];
default_name(end) = [];
default_name = [default_name '_reg'];
[f,d] = uiputfile([dd filesep '*.mat'],'Save...',[dd filesep default_name '.mat']);
if d ~= 0
fnames = fieldnames(handles);
s_idx = find(cellfun(@(x) strcmp(x,'files'),fnames));
regi = [];
for fn = s_idx:numel(fnames)
regi.dat.(fnames{fn}) = handles.(fnames{fn});
end
regi.dat.overlapping_rois(1,:) = [];
regi.dat.p_overlaps(1) = [];
regi.rois.idcs = regi.dat.overlapping_rois;
regi.targets.idcs = regi.dat.targets_s2p_rois;
regi.rois.iscell_idcs = 0 * regi.dat.overlapping_rois;
regi.targets.iscell_idcs = nan * regi.dat.targets_s2p_rois;
for i = 1:numel(regi.dat.files)
for r = 1:size(regi.dat.overlapping_rois(:,i))
regi.rois.iscell_idcs(r,i) = find(handles.files(i).iscell == regi.dat.overlapping_rois(r,i));
end
if handles.targets_loaded
for t = 1:size(regi.dat.targets_s2p_rois(:,i))
if ~isnan(regi.dat.targets_s2p_rois(t,i))
regi.targets.iscell_idcs(t,i) = find(handles.files(i).iscell == regi.dat.targets_s2p_rois(t,i));
end
end
end
end
if handles.targets_loaded
regi.targets.iscell_idcs(:,3) = regi.dat.targets_s2p_rois(:,3);
end
save([d filesep f],'regi');
end
else
uiwait(msgbox('No data loaded - please load at least 1 session before trying to save', 'Error','error'));
end
% --- Executes on key press with focus on figure1 and none of its controls.
function figure1_KeyPressFcn(hObject, eventdata, handles)
% hObject handle to figure1 (see GCBO)
% eventdata structure with the following fields (see MATLAB.UI.FIGURE)
% Key: name of the key that was pressed, in lower case
% Character: character interpretation of the key(s) that was pressed
% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles structure with handles and user data (see GUIDATA)
if isstrprop(eventdata.Key,'digit')
num = str2num(eventdata.Key);
if max([1:handles.files(handles.displayed_image).num_masks] == num) == 1
handles.displayed_mask = num;
handles.(handles.mask_fields{handles.mask_field_nums == num}).BackgroundColor = handles.bg_color(2,:);
off = handles.mask_fields(handles.mask_field_nums ~= num);
for i = 1:numel(off)
handles.(off{i}).BackgroundColor = handles.bg_color(1,:);
end
update_displays(hObject,handles);
end
else
switch eventdata.Key
% case '1'
% handles.displayed_mask = 2;
% update_displays(hObject,handles);
% case '2'
% handles.displayed_mask = 5;
% update_displays(hObject,handles);
case 'p'
handles.proc_flag = ~(handles.proc_flag-1)+1;
handles.proc_text.BackgroundColor = handles.bg_color(handles.proc_flag,:);
update_displays(hObject,handles);
case 'q'
handles.im_flag = true;
handles.displayed_image = 1;
handles.ROI_text1.BackgroundColor = handles.bg_color(1,:);
handles.ROI_text2.BackgroundColor = handles.bg_color(1,:);
handles.day_text1.BackgroundColor = handles.bg_color(2,:);
handles.day_text2.BackgroundColor = handles.bg_color(1,:);
update_displays(hObject,handles);
case 'w'
handles.im_flag = true;
handles.displayed_image = 2;
handles.ROI_text1.BackgroundColor = handles.bg_color(1,:);
handles.ROI_text2.BackgroundColor = handles.bg_color(1,:);
handles.day_text1.BackgroundColor = handles.bg_color(1,:);
handles.day_text2.BackgroundColor = handles.bg_color(2,:);
update_displays(hObject,handles);
case 'a'
handles.im_flag = false;
handles.displayed_image = 1;
handles.ROI_text1.BackgroundColor = handles.bg_color(2,:);
handles.ROI_text2.BackgroundColor = handles.bg_color(1,:);
handles.day_text1.BackgroundColor = handles.bg_color(1,:);
handles.day_text2.BackgroundColor = handles.bg_color(1,:);
update_displays(hObject,handles);
case 's'
handles.im_flag = false;
handles.displayed_image = 2;
handles.ROI_text1.BackgroundColor = handles.bg_color(1,:);
handles.ROI_text2.BackgroundColor = handles.bg_color(2,:);
handles.day_text1.BackgroundColor = handles.bg_color(1,:);
handles.day_text2.BackgroundColor = handles.bg_color(1,:);
update_displays(hObject,handles);
case 'o'
handles.overlay = ~handles.overlay;
handles.cursor_overlay_text.BackgroundColor = handles.bg_color(handles.overlay+1,:);
guidata(hObject,handles)
if handles.overlay
order = [1 0];
C = get (handles.image_axis, 'CurrentPoint');
C = C(1,1:2);
if (C(1) > handles.files(1).dims(1) | C(2) > handles.files(1).dims(2)) || min(C)<0
handles.cursors(2).scatter.XData = nan;
handles.cursors(2).scatter.YData = nan;
C = get (handles.roi_axis, 'CurrentPoint');
C = C(1,1:2);
idcs = (~order)+1;
else
idcs = order+1;
end
if (C(1) <= handles.files(idcs(1)).dims(1) | C(2) <= handles.files(idcs(1)).dims(2)) || min(C)>0
handles.cursors(idcs(1)).scatter.XData = C(1,1);
handles.cursors(idcs(1)).scatter.YData = C(1,2);
else
handles.cursors(idcs(1)).scatter.XData = nan;
handles.cursors(idcs(1)).scatter.YData = nan;
end
else
for i = 1:numel(handles.cursors)
handles.cursors(i).scatter.XData = nan;
handles.cursors(i).scatter.YData = nan;
end
end
end
if ~isempty(handles.tformed_targets_yx) && max(handles.selected_targets) == 1
switch eventdata.Key
case 'downarrow'
if max(handles.tformed_targets_yx(handles.selected_targets,1)+1) < handles.files(handles.displayed_image).dims(1) %513
handles.tformed_targets_yx(handles.selected_targets,1) = handles.tformed_targets_yx(handles.selected_targets,1)+1;
end
handles.plotted_targets.XData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,2);
handles.plotted_targets.YData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,1);
case 'uparrow'
if min(handles.tformed_targets_yx(handles.selected_targets,1)-1) > 0
handles.tformed_targets_yx(handles.selected_targets,1) = handles.tformed_targets_yx(handles.selected_targets,1)-1;
end
handles.plotted_targets.XData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,2);
handles.plotted_targets.YData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,1);
case 'leftarrow'
if min(handles.tformed_targets_yx(handles.selected_targets,2)-1) > 0
handles.tformed_targets_yx(handles.selected_targets,2) = handles.tformed_targets_yx(handles.selected_targets,2)-1;
end
handles.plotted_targets.XData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,2);
handles.plotted_targets.YData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,1);
case 'rightarrow'
if max(handles.tformed_targets_yx(handles.selected_targets,2)+1) < handles.files(handles.displayed_image).dims(2) %513
handles.tformed_targets_yx(handles.selected_targets,2) = handles.tformed_targets_yx(handles.selected_targets,2)+1;
end
handles.plotted_targets.XData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,2);
handles.plotted_targets.YData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,1);
case {'escape' 'return'}
handles.selected_targets = false(numel(handles.selected_targets),1);
handles.plotted_targets.CData(:,2) = handles.selected_targets;
case 'd'
handles.tformed_targets_yx(handles.selected_targets,:) = handles.tformed_targets_default(handles.selected_targets,:);
handles.plotted_targets.XData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,2);
handles.plotted_targets.YData(handles.selected_targets) = handles.tformed_targets_yx(handles.selected_targets,1);
end
if handles.targets_overlapped
handles = detect_target_overlap(handles);
end
end
end
guidata(hObject,handles)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% CustomFunctions %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function handles = adjust_contrast(hObject,event);
handles = guidata(hObject);
if handles.im_flag
max_cont = 10;
slid_cont = hObject.Value;
if slid_cont == 0
slid_cont = 0.001;
elseif slid_cont == 1
slid_cont = 0.999;
end
cont = max_cont * (1-slid_cont);
handles.files(handles.displayed_image).lims{handles.proc_flag}(handles.displayed_mask,:) ...
= get_lims(handles.files(handles.displayed_image).image{handles.proc_flag}(:,:,handles.displayed_mask),cont);
handles.image_display.Parent.CLim = handles.files(handles.displayed_image).lims{handles.proc_flag}(handles.displayed_mask,:);
end
guidata(hObject,handles)
function lims = get_lims(I,cont)
mu = median(I(:));
sd1 = mean(abs(I(I<mu+1e-7) - mu));
sd2 = 1e-7 + mean(abs(I(I>mu-1e-7) - mu));
lims = mu + cont*[-sd1 sd2];
function handles = load_s2p_struct(hObject,handles,idx)
[f,d] = uigetfile('*.*');
if f~=0
handles = set_gui_defaults(hObject,handles);
handles.files(idx).filepath = [d f];
handles.fixed_textbox.String = handles.files(1).filepath;
handles.moving_textbox.String = handles.files(2).filepath;
[~,~,ext] = fileparts(handles.files(idx).filepath);
switch ext
case '.mat'
try
load(handles.files(idx).filepath);
handles.files(idx).dims = size(dat.ops.mimg1);
handles.files(idx).dims = handles.files(idx).dims(1:2);
%handles.files(idx).num_masks = size(dat.mimg,3);
handles.files(idx).num_masks = 6;
handles.files(idx).image{1} = zeros(handles.files(idx).dims(1),handles.files(idx).dims(2),handles.files(idx).num_masks);
handles.files(idx).image{2} = zeros(handles.files(idx).dims(1),handles.files(idx).dims(2),handles.files(idx).num_masks);
handles.files(idx).lims{1} = zeros(handles.files(idx).num_masks,2);
handles.files(idx).lims{2} = zeros(handles.files(idx).num_masks,2);
[xx,yy] = meshgrid(dat.ops.xrange,dat.ops.yrange);
im_idcs = sub2ind(size(handles.files(idx).image{1}(:,:,1)),yy,xx);
pixels_per_im = handles.files(idx).dims(1) * handles.files(idx).dims(2);
% for i = 1:handles.files(idx).num_masks
% handles.files(idx).image{1}(im_idcs + ((i-1)*pixels_per_im)) = dat.mimg(:,:,i);
% handles.files(idx).image{2}(im_idcs + ((i-1)*pixels_per_im)) = dat.mimg_proc(:,:,i);
% end
% ROI_text1 im
i = 1;
handles.files(idx).image{1}(im_idcs + ((i-1)*pixels_per_im)) = dat.mimg(:,:,2);
handles.files(idx).image{2}(im_idcs + ((i-1)*pixels_per_im)) = dat.mimg_proc(:,:,2);
handles.files(idx).lims{1}(i,:) = get_lims(dat.mimg(:,:,2),5);
handles.files(idx).lims{2}(i,:) = get_lims(dat.mimg_proc(:,:,2),5);
% corr im
i = 2;
handles.files(idx).image{1}(im_idcs + ((i-1)*pixels_per_im)) = dat.mimg(:,:,5);
handles.files(idx).image{2}(im_idcs + ((i-1)*pixels_per_im)) = dat.mimg_proc(:,:,5);
handles.files(idx).lims{1}(i,:) = get_lims(dat.mimg(:,:,5),5);
handles.files(idx).lims{2}(i,:) = get_lims(dat.mimg_proc(:,:,5),5);
% sd im
i = 3;
handles.files(idx).image{1}(im_idcs + ((i-1)*pixels_per_im)) = dat.ops.sdmov;
handles.files(idx).image{2}(im_idcs + ((i-1)*pixels_per_im)) = dat.ops.sdmov;
handles.files(idx).lims{1}(i,:) = get_lims(dat.ops.sdmov,5);
handles.files(idx).lims{2}(i,:) = get_lims(dat.ops.sdmov,5);
% corr im
i = 4;
handles.files(idx).image{1}(im_idcs + ((i-1)*pixels_per_im)) = dat.res.iclust;
handles.files(idx).image{2}(im_idcs + ((i-1)*pixels_per_im)) = dat.res.iclust;
handles.files(idx).lims{1}(i,:) = [min(dat.res.iclust(:)) max(dat.res.iclust(:))];
handles.files(idx).lims{2}(i,:) = [min(dat.res.iclust(:)) max(dat.res.iclust(:))];
% skewness im
i = 5;
handles.files(idx).image{1}(im_idcs + ((i-1)*pixels_per_im)) = dat.res.lambda;
handles.files(idx).image{2}(im_idcs + ((i-1)*pixels_per_im)) = dat.res.lambda0;
handles.files(idx).lims{1}(i,:) = get_lims(dat.res.lambda,5);
handles.files(idx).lims{2}(i,:) = get_lims(dat.res.lambda0,5);
% red im
i = 6;
handles.files(idx).image{1}(im_idcs + ((i-1)*pixels_per_im)) = dat.mimg(:,:,3);
handles.files(idx).image{2}(im_idcs + ((i-1)*pixels_per_im)) = dat.mimg_proc(:,:,3);
handles.files(idx).lims{1}(i,:) = get_lims(dat.mimg(:,:,3),5);
handles.files(idx).lims{2}(i,:) = get_lims(dat.mimg_proc(:,:,3),5);
handles.files(idx).default_image = handles.files(idx).image;
handles = set_gui_defaults(hObject,handles);
handles = reload_roi_defaults(handles);
if handles.targets_loaded && handles.targets_overlapped
handles = reset_targets_overlap(handles);
end
[handles.files(idx).rois_ibar,handles.files(idx).centroids,handles.files(1).roi_areas,handles.files(idx).iscell] = load_S2P_rois(dat,handles.files(idx).dims);
handles.files(idx).roi_idcs = unique(handles.files(idx).rois_ibar(:,4),'stable');
handles.files(idx).num_rois = numel(unique(handles.files(idx).rois_ibar(:,4)));
handles.files(idx).roi_status = [ones(size(handles.files(idx).rois_ibar,1),1) zeros(size(handles.files(idx).rois_ibar,1),1)];
handles.files(idx).default_rois_ibar = handles.files(idx).rois_ibar;
handles.files(idx).default_centroids = handles.files(idx).centroids;
handles.files(idx).default_roi_areas = handles.files(idx).roi_areas;
handles.files(idx).default_roi_idcs = handles.files(idx).roi_idcs;
handles.files(idx).loaded = true;
catch
warning('Import error - .mat file is not of the correct format, cannot load')
end
case {'.tif' '.tiff'}
handles.files(idx).image = imread(handles.files(idx).filepath);
handles.files(idx).dims = size(handles.files(idx).image);
handles.files(idx).loaded = true;
handles.files(idx).default_image = handles.files(idx).image;
end
handles.displayed_image = idx;
initialize_displays(hObject,handles);
update_displays(hObject,handles);
end
function handles = set_gui_defaults(hObject,handles)
handles.selected_rois = [];
handles.overlapping_rois = [nan nan];
handles.p_overlaps = [nan];
guidata(hObject,handles);
function select_rois(hObject,eventdata)
handles = guidata(hObject);
if eventdata.Button == 1 && ~isempty(handles.files(1).rois_ibar) && ~isempty(handles.files(2).rois_ibar)
file_idcs = 1:numel(handles.files);
idx = sub2ind(handles.files(1).dims,round(eventdata.IntersectionPoint(2)),round(eventdata.IntersectionPoint(1)));
handles.selected_rois = [];
for i = 1:numel(handles.files)
if ~isempty(handles.files(i).rois_ibar(handles.files(i).rois_ibar(:,1) == idx,end))
handles.selected_rois = [handles.selected_rois ; ...
(i + (0*handles.files(i).rois_ibar(handles.files(i).rois_ibar(:,1) == idx,end))) ...
handles.files(i).rois_ibar(handles.files(i).rois_ibar(:,1) == idx,end)];
end
end
if ~isempty(handles.selected_rois)
num_selected = size(handles.selected_rois,1);
centroids_yx = zeros(num_selected,2);
for r = 1:num_selected
%centroids_yx(r,:) = handles.files(handles.selected_rois(r,1)).centroids(handles.selected_rois(r,2),:);
% Added 20170511 HD to fix roi indexing
centroids_yx(r,:) = handles.files(handles.selected_rois(r,1)).centroids(handles.files(handles.selected_rois(r,1)).roi_idcs == handles.selected_rois(r,2),:);
end
[~,min_dist_idx] = eudist(centroids_yx,eventdata.IntersectionPoint([2 1]));
handles.selected_rois = handles.selected_rois(min_dist_idx,:);
this_file = file_idcs(file_idcs==handles.selected_rois(1));
other_file = file_idcs(file_idcs~=handles.selected_rois(1));
[~,overlap_candidate] = eudist(handles.files(other_file).centroids,centroids_yx(min_dist_idx,:));
overlap_candidate = handles.files(other_file).roi_idcs(overlap_candidate); % Added 20170511 HD to correct roi indexing
these_idcs = handles.files(this_file).rois_ibar(:,4)==handles.selected_rois(2);
other_idcs = handles.files(other_file).rois_ibar(:,4)==overlap_candidate;
overlap_p = calculate_overlap(handles.files(this_file).rois_ibar(these_idcs,1),handles.files(other_file).rois_ibar(other_idcs,1));
if overlap_p > 0
if (handles.overlapping_rois(:,other_file) == overlap_candidate) == (handles.overlapping_rois(:,this_file) == handles.selected_rois(2))
if max(handles.overlapping_rois(:,other_file) == overlap_candidate) == 1
toremove = handles.overlapping_rois(:,this_file) == handles.selected_rois(2);
handles.overlapping_rois(toremove,:) = [];
handles.p_overlaps(toremove) = [];
else
handles.overlapping_rois = [handles.overlapping_rois ; 0 0];
handles.overlapping_rois(end,[this_file other_file]) = [handles.selected_rois(2) overlap_candidate];
handles.p_overlaps = [handles.p_overlaps ; overlap_p];
end
else
prev_selected = [find(handles.overlapping_rois(:,this_file) == handles.selected_rois(2)) ; ...
find(handles.overlapping_rois(:,other_file) == overlap_candidate)];
for i = 1:size(prev_selected,1)
for j = 1:size(handles.overlapping_rois,2)
prev_roi = handles.overlapping_rois(prev_selected(i),j);
prev_idcs = handles.files(j).rois_ibar(:,4)==prev_roi;
handles.files(j).roi_status(prev_idcs,:) = [1+(0*handles.files(j).roi_status(prev_idcs,1)) (0*handles.files(j).roi_status(prev_idcs,2))];
end
end
handles.overlapping_rois(prev_selected,:) = [];
handles.overlapping_rois = [handles.overlapping_rois ; 0 0];
handles.overlapping_rois(end,[this_file other_file]) = [handles.selected_rois(2) overlap_candidate];
handles.p_overlaps(prev_selected) = [];
handles.p_overlaps = [handles.p_overlaps ; overlap_p];
end
handles.files(this_file).roi_status(these_idcs,:) = ~handles.files(this_file).roi_status(these_idcs,:);
handles.files(other_file).roi_status(other_idcs,:) = ~handles.files(other_file).roi_status(other_idcs,:);
update_displays(hObject,handles);
if handles.targets_overlapped
handles = detect_target_overlap(handles);
end
end
end
end
guidata(hObject,handles)
function handles = reload_roi_defaults(handles)
for i = 1:numel(handles.files)
handles.files(i).image = handles.files(i).default_image;
handles.files(i).dims = handles.files(i).dims;
handles.files(i).rois_ibar = handles.files(i).default_rois_ibar;
handles.files(i).centroids = handles.files(i).default_centroids;
handles.files(i).roi_idcs = handles.files(i).default_roi_idcs;
handles.files(i).roi_areas = handles.files(i).default_roi_areas;
handles.files(i).num_rois = numel(handles.files(i).roi_idcs);
handles.files(i).roi_status = [ones(size(handles.files(i).rois_ibar,1),1) zeros(size(handles.files(i).rois_ibar,1),1)];
end
handles.overlapping_rois = [nan nan];
handles.p_overlaps = [nan];
function handles = lasso_targets(hObject,~,~)
handles = guidata(hObject);
if size(handles.tformed_targets_yx,1) > 1
if max(handles.selected_targets) == 0
try
handles.plotted_targets.CData(:,2) = 0;
lasso_selected = imfreehand(gca);
lasso_area = wait(lasso_selected);
handles.selected_targets = 0 * handles.selected_targets;
handles.selected_targets = inpolygon(handles.tformed_targets_yx(:,2),handles.tformed_targets_yx(:,1),lasso_area(:,1),lasso_area(:,2));
delete(lasso_selected);
handles.plotted_targets.CData(:,2) = handles.selected_targets;
end
else
p = get(gca,'CurrentPoint');
s = handles.selected_targets;
yx = [handles.plotted_targets.YData' handles.plotted_targets.XData'];
set(gcf,'WindowButtonMotionFcn',{@drag, handles, p, yx, s})
end
guidata(hObject,handles);
end
function drag(hObject,event,handles,p,yx,s)
np = get(gca,'CurrentPoint');
dyx = np(1,[2 1])- p(1,[2 1]);
nyx = bsxfun(@plus,yx,dyx);
% Added HD 20170510
nyx(nyx<=0) = 1;
nyx(nyx(:,1)>handles.files(handles.displayed_image).dims(1),1) = handles.files(handles.displayed_image).dims(1);
nyx(nyx(:,2)>handles.files(handles.displayed_image).dims(2),2) = handles.files(handles.displayed_image).dims(2);
handles.tformed_targets_yx(s,:) = nyx(s,:);
handles.plotted_targets.XData(s) = nyx(s,2);
handles.plotted_targets.YData(s) = nyx(s,1);
if handles.targets_overlapped
handles = detect_target_overlap(handles);
end
guidata(hObject,handles);
function [handles] = plot_targets(hObject,handles)
for i = 1:numel(handles.dil_targets_handles)
delete(handles.dil_targets_handles(i));
end
[handles.dil_targets_handles,handles.dil_targets_yx,~] = draw_rois_local(handles.tformed_targets_yx,handles.image_axis,handles.files(handles.displayed_image).dims,'Color',[0.6 0.6 0.6]);
handles.original_targets.XData = handles.tformed_targets_default(:,2);
handles.original_targets.YData = handles.tformed_targets_default(:,1);
handles.plotted_targets.XData = handles.tformed_targets_yx(:,2);
handles.plotted_targets.YData = handles.tformed_targets_yx(:,1);
handles.plotted_targets.SizeData = handles.target_sizes(handles.targets_s2p_rois(:,3)+1);
handles.plotted_targets.CData = repmat([1 0 0],size(handles.tformed_targets_yx,1),1);
for i = 1:numel(handles.targets)
handles.targets(i).scatter.XData = handles.files(i).targets_overlap_yx(:,2);
handles.targets(i).scatter.YData = handles.files(i).targets_overlap_yx(:,1);
end
guidata(hObject,handles);
function [handles] = reset_targets(hObject,handles);
for i = 1:numel(handles.dil_targets_handles)
delete(handles.dil_targets_handles(i));
end
handles.dil_targets_handles = [];
handles.original_targets.XData = [];
handles.original_targets.YData = [];
handles.plotted_targets.XData = [];
handles.plotted_targets.YData = [];
handles.plotted_targets.SizeData = handles.target_sizes(1);
handles.plotted_targets.CData = [1 0 1];
for i = 1:numel(handles.targets)
handles.targets(i).scatter.XData = [];
handles.targets(i).scatter.YData = [];
end
guidata(hObject,handles);
function [handles] = transform_rois(handles,idx)
tformed_ibar = [];
handles.files(idx).centroids = [];
handles.files(idx).roi_areas = [];
for r = 1:handles.files(idx).num_rois
blank_im = 0 * handles.files(idx).image{1}(:,:,1);
r_idcs = handles.files(idx).rois_ibar(:,4) == handles.files(idx).roi_idcs(r) & handles.files(idx).rois_ibar(:,3) == 1; % "& handles.files(idx).rois_ibar(:,3) == 1" Added 20170517 HD to fix ROI growing post transform