WSG_v.1.05 software for neural structure morphometry, including on-chip mapping

WSG_v.1.05 software for neural structure morphometry, including on-chip mapping

Citation Author(s):
Alexander
Notchenko
Oleg
Gradov
Submitted by:
Oleg Gradov
Last updated:
Wed, 01/16/2019 - 03:45
DOI:
10.21227/fnrx-3t19
License:
Dataset Views:
28
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Abstract: 

This code was used in some previous our articles, such as:

  • A. V. Notchenko and O. V. Gradov. A five-axis arm-manipulator laser system & an algorithm for digital processing of output data for recording and morpho-topological identification of cells and tissue structures. Visualization, Image Processing and Computation in Biomedicine, 2(1), 2013. DOI: 10.1615/VisualizImageProcComputatBiomed.2013005967
  • A. V. Notchenko and O. V. Gradov. Elementary morphometric labs-on-a-chip based on hemocytometric chambers with radiofrequency culture identification and relay of spectrozonal histochemical monitoring. Visualization, Image Processing and Computation in Biomedicine, 2(1), 2013. DOI: 10.1615/VisualizImageProcComputatBiomed.2013005968
Instructions: 

 

function varargout = weight_sweep_gui(varargin)

% WEIGHT_SWEEP_GUI M-file for weight_sweep_gui.fig

%      WEIGHT_SWEEP_GUI, by itself, creates a new WEIGHT_SWEEP_GUI or raises the existing

%      singleton*.

%

%      H = WEIGHT_SWEEP_GUI returns the handle to a new WEIGHT_SWEEP_GUI or the handle to

%      the existing singleton*.

%

%      WEIGHT_SWEEP_GUI('CALLBACK',hObject,eventData,handles,...) calls the local

%      function named CALLBACK in WEIGHT_SWEEP_GUI.M with the given input arguments.

%

%      WEIGHT_SWEEP_GUI('Property','Value',...) creates a new WEIGHT_SWEEP_GUI or raises the

%      existing singleton*.  Starting from the left, property value pairs are

%      applied to the GUI before weight_sweep_gui_OpeningFcn gets called.  An

%      unrecognized property name or invalid value makes property application

%      stop.  All inputs are passed to weight_sweep_gui_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 weight_sweep_gui

% Last Modified by GUIDE v2.5 16-Oct-2011 12:00:46

% Begin initialization code - DO NOT EDIT

gui_Singleton = 1;

gui_State = struct('gui_Name',       mfilename, ...

    'gui_Singleton',  gui_Singleton, ...

    'gui_OpeningFcn', @weight_sweep_gui_OpeningFcn, ...

    'gui_OutputFcn',  @weight_sweep_gui_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

end

% --- Executes just before weight_sweep_gui is made visible.

function weight_sweep_gui_OpeningFcn(hObject, ~, handles, varargin)

% This function has no output args, see OutputFcn.

% varargin   command line arguments to weight_sweep_gui (see VARARGIN)

% Choose default command line output for weight_sweep_gui

handles.output = hObject;

% Update handles structure

guidata(hObject, handles);

% UIWAIT makes weight_sweep_gui wait for user response (see UIRESUME)

% uiwait(handles.figure1);

set(handles.imag_axes,'xticklabel',[],'xticklabelmode','manual','yticklabel'...

    ,[],'yticklabelmode','manual','Ticklength',[0 0],'tag','imag_axes');

set(handles.proc_axes,'xticklabel',[],'xticklabelmode','manual','yticklabel'...

    ,[],'yticklabelmode','manual','Ticklength',[0 0],'tag','proc_axes'...

    ,'ButtonDownFcn',@SelCon);%,'NextPlot','Replacechildren');

set(hObject,'name','CellCounter v1');

%---------------------------------------------------------

clear global mcount;

global figz;

figz=zoom;

set(figz,'ActionPostCallback',@zoom_callback,'enable','off');

%---------------------------------------------------------

end

% --- Outputs from this function are returned to the command line.

function varargout = weight_sweep_gui_OutputFcn(~, ~, handles)

% varargout  cell array for returning output args (see VARARGOUT)

% Get default command line output from handles structure

varargout{1} = handles.output;

end

% --- Executes on slider movement.

%------------------SLIDERS-------------------------------------------------

function red_slider_Callback(~, ~, handles)

% Hints: get(hObject,'Value') returns position of slider

%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

%disp(get(hObject,'value'));

refpic(handles);

end

function red_slider_CreateFcn(hObject, ~, ~)

% Hint: slider controls usually have a light gray background.

if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor',[.9 .9 .9]);

end

end

function green_slider_Callback(~, ~, handles)

% Hints: get(hObject,'Value') returns position of slider

%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

refpic(handles);

end

function green_slider_CreateFcn(hObject, ~, ~)

% Hint: slider controls usually have a light gray background.

if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor',[.9 .9 .9]);

end

end

function blue_slider_Callback(~, ~, handles)

% Hints: get(hObject,'Value') returns position of slider

%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

refpic(handles);

end

function blue_slider_CreateFcn(hObject, ~, ~)

% Hint: slider controls usually have a light gray background.

if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor',[.9 .9 .9]);

end

end

%------------------LISTBOX-------------------------------------------------

function pic_list_Callback(hObject, ~, handles)

% Hints: contents = cellstr(get(hObject,'String')) returns pic_list contents as cell array

%        contents{get(hObject,'Value')} returns selected item from pic_list

axes(handles.imag_axes);

selected_position=get(hObject,'value');

names=get(hObject,'string');

imdata=imread([get(handles.folder_edit,'string'),names{selected_position}]);

image(imdata);

set(handles.imag_axes,'xticklabel',[],'yticklabel',[],'Ticklength',[0 0],'userdata',imdata);

title(names{selected_position});

refpic(handles);

end

function pic_list_CreateFcn(hObject, ~, ~)

% Hint: listbox 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

end

%------------------TEXT_EDIT-----------------------------------------------

function folder_edit_Callback(~, ~, ~)

% Hints: get(hObject,'String') returns contents of folder_edit as text

%        str2double(get(hObject,'String')) returns contents of folder_edit as a double

end

function folder_edit_CreateFcn(hObject, ~, ~)

% 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

end

%------------------BUTTONS-------------------------------------------------

function scan_button_Callback(hObject,eventdata, handles)

folder_way=get(handles.folder_edit,'string');

if folder_way(end)~='\'

    folder_way=[folder_way,'\'];

    set(handles.folder_edit,'string',folder_way);

end

direc=dir(folder_way);

names={};

for i=3:length(direc)

    temp_var=direc(i).name(end-2:end);

    if strcmp(temp_var,'jpg')||strcmp(temp_var,'tif')||strcmp(temp_var,'bmp')||strcmp(temp_var,'png')

        names=cat(2,names,{direc(i).name});

    end

end

if isempty(names)

    return

end

%sorting names array with numerical substrings

for i=1:length(names)

    temp_var=[];

    for j=1:size(names{i},2)

        if (int16(names{i}(j))>=48)&&(int16(names{i}(j))<=57)

            temp_var=[temp_var,names{i}(j)];

        end

    end

    num_var(i)=str2double(temp_var);

end

[~,perm]=sort(num_var);

clear num_var temp_var not_var ;

names=names(perm);

set(handles.pic_list,'string',names);

end

function anim_button_Callback(~, ~, handles)

names=get(handles.pic_list,'string');

images=cell(size(names));

for i=1:length(names)

    images{i}=imread([get(handles.folder_edit,'string'),names{i}]);

end

axes(handles.imag_axes);

for i=1:12

    image(images{i});

    set(handles.imag_axes,'xticklabel',[],'yticklabel',[]);

    title(names{i});

    pause(1/1.5);

end

end

function smoothbtn_Callback(~, ~, ~)

% F = [.05 .1 .05; .1 .4 .1; .05 .1 .05];

% ZC = conv2(ZN,F,'same');

disp('derp_write_a_function');

end

%------------------List----------------------------------------------------

function lvlsld_Callback(hObject, eventdata, handles)

refpic(handles);

end

function lvlsld_CreateFcn(hObject, eventdata, handles)

if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor',[.9 .9 .9]);

end

end

%------------------Falling_List--------------------------------------------

% --- Executes on selection change in contour_width.

function contour_width_Callback(~, ~, handles)

refpic(handles);

end

function contour_width_CreateFcn(hObject, ~, ~)

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end

end

%------------------checkboxes----------------------------------------------

function checkbox1_Callback(hObject, eventdata, handles)

 

end

%------------------other_functions-----------------------------------------

function refpic(handles)

axes(handles.proc_axes);

names=get(handles.pic_list,'string');

if ~isempty(names)

    way=[get(handles.folder_edit,'string'),names{get(handles.pic_list,'value')}];

else

    errordlg('Image files most be loaded with SCAN !');

    return

end

pic=imread(way);

I = get(handles.red_slider,'value')*pic(:,:,1)+get(handles.green_slider,'value')...

    *pic(:,:,2)+get(handles.blue_slider,'value')*pic(:,:,3);

imagesc(max(max(I))-I);hold on;

sli_lvl=double(min(min(I))+(max(max(I))-min(min(I)))*get(handles.lvlsld,'Value'));

%n_sli=get(handles.n_of_slices,'Value');

l_wid=1+(get(handles.contour_width,'value')-1)/2;

if get(handles.lvlsld,'Value')~=0

    [conar,conhand]=imcontour(I,[sli_lvl 0]); hold off;

end

set(findobj('type','hggroup'),'linewidth',l_wid);

set(handles.proc_axes,'xticklabel',[],'yticklabel',[],'Ticklength',[0 0],...

    'ButtonDownFcn',@SelCon,'xlim',get(handles.imag_axes,'xlim')...

    ,'ylim',get(handles.imag_axes,'ylim'));

set(handles.proc_axes,'userdata',max(max(I))-I);

set(handles.imag_axes,'tag','imag_axes');

set(handles.proc_axes,'tag','proc_axes');

achpa=allchild(handles.proc_axes);

for i=achpa

    set(i,'hittest','off');

end

%set(findobj(gcf,'tag','proc_axes'),'ButtonDownFcn',@SelCon);

% set(handles.slid_value,'string',...

%     num2str([get(handles.red_slider,'value'),get(handles.green_slider,'value')...

%     ,get(handles.blue_slider,'value')]));

end

function SelCon(obj,~)

%flag=true;

ut_sel=findobj(get(obj,'parent'),'tag','ut_sel');

proc_axes=obj;

if strcmp(get(ut_sel,'state'),'on')

    cp=get(proc_axes,'currentpoint');

    cp=cp(1,1:2)';

    chlist=allchild(findobj('type','hggroup'));

    mincon=cell(size(chlist));

    mindist=zeros(size(chlist));

    for i=1:length(chlist)

        mincon{i}=[get(chlist(i),'xdata')';get(chlist(i),'ydata')'];

        %mindist(i)=min(min(abs(mincon{i}-cp*ones(1,length(mincon{i})))));

        mindist(i)=min(sum((mincon{i}-cp*ones(1,length(mincon{i}))).^2,1));

    end

    mini=find(mindist==min(mindist));

    axes(proc_axes);hold on;

    plot(mincon{mini(1)}(1,:),mincon{mini(1)}(2,:),'linewidth',3,...

        'color',[0 0 0]);

    hold off;

    centpoint=mean(mincon{mini}(:,1:end-1),2);

    contarea=polyarea(mincon{mini}(1,1:end-1),mincon{mini}(2,1:end-1));

    text(centpoint(1),centpoint(2),num2str(contarea),...

        'LineWidth',2,'color','white','FontSize',12,...

        'parent',proc_axes);

end

end

%------------------Zoom_and_toolbar----------------------------------------

function [flag]=zoom_callback(obj,event_obj)

flag=true;

imaxob=findobj(obj,'tag','imag_axes');

praxob=findobj(obj,'tag','proc_axes');

if strcmp(get(event_obj.Axes,'tag'),'imag_axes')

    set(praxob,'xlim',get(event_obj.Axes,'xlim'),'ylim',get(event_obj.Axes,'ylim'));

else

    set(imaxob,'xlim',get(event_obj.Axes,'xlim'),'ylim',get(event_obj.Axes,'ylim'));

end

end

function ut_in_OffCallback(~, ~, handles)

global figz

if strcmp(get(figz,'enable'),'on')&&strcmp(get(figz,'direction'),'in')

    return

else

    set(figz,'enable','off','direction','in');

end

set(handles.imag_axes,'tag','imag_axes');

set(handles.proc_axes,'tag','proc_axes');

end

function ut_in_OnCallback(~, ~, handles)

global figz

set(figz,'enable','on','direction','in');

set(handles.imag_axes,'tag','imag_axes');

set(handles.proc_axes,'tag','proc_axes');

end

function ut_out_OffCallback(~, ~, handles)

global figz

if strcmp(get(figz,'enable'),'on')&&strcmp(get(figz,'direction'),'out')

    return

else

    set(figz,'enable','off','direction','out');

end

set(handles.imag_axes,'tag','imag_axes');

set(handles.proc_axes,'tag','proc_axes');

end

function ut_out_OnCallback(~, ~, handles)

global figz

set(figz,'enable','on','direction','out');

set(handles.imag_axes,'tag','imag_axes');

set(handles.proc_axes,'tag','proc_axes');

end

function dir_btn_Callback(~, ~, handles)

folder_name = uigetdir(cd);

set(handles.folder_edit,'string',folder_name);

end

function tbbtn_Callback(hObject, eventdata, handles)

if ~isempty(findobj('name','contour information'))

    delete(findobj('name','contour information')); 

end

if get(handles.lvlsld,'Value')==0

    errordlg('select contouring level!');

    return   

end

tbfg=figure('name','contour information','position',[403   246   840   420],'resizefcn',@figure1_ResizeFcn);

chlist=allchild(findobj(handles.proc_axes,'type','hggroup'));

dat=cell(length(chlist),2);

for i=1:length(chlist)

    dat{i,1}=i;

    xd=get(chlist(i),'xdata');

    yd=get(chlist(i),'ydata');

    dat{i,2}=polyarea(xd(1:end-1),yd(1:end-1));

end

columnname={'contour number' , 'area'};

columnformat = {'numeric','numeric'};

columneditable =  [false false];

tbhand = uitable(tbfg,'Units','normalized','Position',[.05 .05 .3 .9],...

    'Data', dat,'ColumnName', columnname,...

    'ColumnFormat', columnformat,...

    'ColumnEditable', columneditable,...

    'RowName',[],'userdata', dat,...

    'CellSelectionCallback',@rscb);

ex=get(tbhand,'extent');

tbpos=get(tbhand,'position');

tbpos(3)=ex(3);%+.028;

set(tbhand,'position',tbpos);

minarhand=uicontrol('tag','ed1','style','edit','units','normalized','position',...

    [sum(tbpos([1,3]))+.05 .05 .1 .05],'string','400','callback',@slcb);

maxarhand=uicontrol('tag','ed2','style','edit','units','normalized','position',...

    [sum(tbpos([1,3]))+.2 .05 .1 .05],'string','5000','callback',@slcb);

slcb();

miapos=get(minarhand,'position');

%maapos=get(maxarhand,'position');

tpapos=[sum(tbpos([1,3]))+.05 sum(miapos([2,4]))+.05 0 0]; 

tpapos(3)=(1-tpapos(1)+.025)/2-.05;

tpapos(4)=(1-tpapos(2)-.05);

tiapos=tpapos;

tiapos(1)=sum(tpapos([1,3]))+.025;

tab_proc_axes=axes('xticklabel',[],'xticklabelmode','manual','yticklabel'...

    ,[],'yticklabelmode','manual','Ticklength',[0 0],'tag','tab_proc_axes'...

    ,'units','normalized','position',tpapos);

tab_imag_axes=axes('xticklabel',[],'xticklabelmode','manual','yticklabel'...

    ,[],'yticklabelmode','manual','Ticklength',[0 0],'tag','tab_imag_axes'...

    ,'units','normalized','position',tiapos);

 

notcellhand=uicontrol('tag','ncb1','style','pushbutton','units','normalized','position',...

    [sum(tbpos([1,3]))+.35 .075 .075 .05],'string','not Cell','callback',@nccb);

isacellhand=uicontrol('tag','icb1','style','pushbutton','units','normalized','position',...

    [sum(tbpos([1,3]))+.425 .075 .075 .05],'string','is a Cell','callback',@iccb);

mancellhand=uicontrol('tag','mcb1','style','pushbutton','units','normalized','position',...

    [sum(tbpos([1,3]))+.35 .025 .15 .05],'string','manual input','callback',@mccb);

 

textboxhand=uicontrol('tag','tb1','style','text','units','normalized','position',...

    [sum(tbpos([1,3]))+.5 .025 .2 .12],'string','select an option');

%------------------------------------------------------------------------

 

%------------------------------------------------------------------------

end

function slcb(obj,event_obj)

tbh=findobj(1,'type','uitable');

tbe1=findobj(1,'tag','ed1');

tbe2=findobj(1,'tag','ed2');

%-------------------------------------------

chlist=allchild(findobj(0,'type','hggroup'));

dat=zeros(length(chlist),2);

for i=1:length(chlist)

    dat(i,1)=i;

    xd=get(chlist(i),'xdata');

    yd=get(chlist(i),'ydata');

    dat(i,2)=polyarea(xd(1:end-1),yd(1:end-1));

end

%-------------------------------------------

%dat=cell2mat(get(tbh,'userdata'));

tdat=dat(:,2)';

val=[str2double(get(tbe1,'string')) str2double(get(tbe2,'string'))];

mask=(tdat<=val(2))&(val(1)<=tdat);

tdat=tdat(mask);

numr=dat(mask',1);

pcdat=[numr,tdat'];

%cdat=mat2cell(pcdat,ones(1,l),[1 1]);

cdat=num2cell(pcdat);

set(tbh,'data',cdat);

end

function rscb(obj,event_obj)

tab_proc_axes=findobj(get(obj,'parent'),'tag','tab_proc_axes');

tab_imag_axes=findobj(get(obj,'parent'),'tag','tab_imag_axes');

proc_axes=get(findobj(0,'type','hggroup'),'parent');

imag_axes=findobj(0,'tag','imag_axes');

imdat=get(proc_axes,'userdata');

fulimdat=get(imag_axes,'userdata');

imsiz=size(imdat);

h=1.5;

global selrow;

try

    selrow=event_obj.Indices(1,1);

catch exception

    return

end

dat=cell2mat(get(obj,'data'));

conum=dat(selrow,1);

%------------------------------------------------------------

chlist=allchild(findobj(0,'type','hggroup'));

mycont=chlist(conum);

xd=get(mycont,'xdata');

yd=get(mycont,'ydata');

imbox=[floor(min(xd)) ceil(max(xd)) floor(min(yd)) ceil(max(yd))];

imagesc(imdat,'parent',tab_proc_axes);

axes(tab_proc_axes);

hold on;plot(xd,yd,'color','k','linewidth',2);hold off;

dh=sum(imbox.*[-1 1 0 0]);dv=sum(imbox.*[0 0 -1 1]);

fr=zeros(1,4);

if imbox(1)-h*dh>1

    fr(1)=floor(imbox(1)-dh);

else

    fr(1)=1;

end

if imbox(2)+h*dh<imsiz(2)

    fr(2)=ceil(imbox(2)+dh);

else

    fr(2)=imsiz(2);

end

if imbox(3)-h*dv>1

    fr(3)=floor(imbox(3)-dv);

else

    fr(3)=1;

end

if imbox(4)+h*dv<imsiz(1)

    fr(4)=ceil(imbox(4)+dv);

else

    fr(4)=imsiz(1);

end

axes(tab_imag_axes);

image(fulimdat);

set(tab_proc_axes,'xlim',fr(1:2),'ylim',fr(3:4));%,'userdata',fr);

set(tab_imag_axes,'xlim',fr(1:2),'ylim',fr(3:4),'userdata',fr);

set(tab_proc_axes,'xticklabel',[],'xticklabelmode','manual','yticklabel'...

    ,[],'yticklabelmode','manual','Ticklength',[0 0],'tag','tab_proc_axes','userdata',mycont);

set(tab_imag_axes,'xticklabel',[],'xticklabelmode','manual','yticklabel'...

    ,[],'yticklabelmode','manual','Ticklength',[0 0],'tag','tab_imag_axes');

end

function nccb(hObject, eventdata, handles)

frame=get(findobj(1,'tag','tab_imag_axes'),'userdata');

if frame

    mycont=get(findobj(1,'tag','tab_proc_axes'),'userdata');

    status='not_cell';

    xyar=[get(mycont,'xdata'),get(mycont,'ydata')]';

    xyar=xyar(:,1:end-1);

    saved_struct=struct('status',status,'contours',{xyar},'frame',frame);

    save_data(saved_struct);

    %--------------------cell removal------------------------------

    global selrow;

    tbh=findobj(1,'type','uitable');

    alldat=cell2mat(get(tbh,'userdata'));

    dat=cell2mat(get(tbh,'data'));

    conum=dat(selrow,1);

    dat=[dat(1:selrow-1,:);dat(selrow+1:end,:)];

    alldat=[alldat(1:conum-1,:);alldat(conum+1:end,:)];

    set(tbh,'data',num2cell(dat),'userData',num2cell(alldat));

    %--------------------END---------------------------------------

else

    errordlg('YOU MUST SELECT SOMETHING IN THE TABLE!');

    return

end 

end

function iccb(hObject, eventdata, handles)

frame=get(findobj(1,'tag','tab_imag_axes'),'userdata');

if frame

    status='is_a_cell';

    mycont=get(findobj(1,'tag','tab_proc_axes'),'userdata');

    xyar=[get(mycont,'xdata'),get(mycont,'ydata')]';

    xyar=xyar(:,1:end-1);

    saved_struct=struct('status',status,'contours',{xyar},'frame',frame);

    save_data(saved_struct);

    %--------------------cell removal------------------------------

    global selrow;

    tbh=findobj(1,'type','uitable');

    alldat=cell2mat(get(tbh,'userdata'));

    dat=cell2mat(get(tbh,'data'));

    conum=dat(selrow,1);

    dat=[dat(1:selrow-1,:);dat(selrow+1:end,:)];

    alldat=[alldat(1:conum-1,:);alldat(conum+1:end,:)];

    set(tbh,'data',num2cell(dat),'userData',num2cell(alldat));

    %--------------------END---------------------------------------

else

    errordlg('YOU MUST SELECT SOMETHING IN THE TABLE!');

    return

end

end

function mccb(hObject, eventdata, handles)

frame=get(findobj(1,'tag','tab_imag_axes'),'userdata');

if frame

    textb=findobj(1,'style','text');

   %-------------------------------------------------------------- 

    global i p n;     

    delete(findobj(handles.figure1,'type','line'));

    i=1;

    n=0;

    p=[];

    firsttext='Выделете первый контур (ставить точки нажатием левой клавиши мыши)  по часовой стрелке. когда закончите нажмите пробел';

    set(textb,'String',firsttext);

    

    set(handles.mainaxes,'buttonDownFcn',@clickfcn);%,'nextplot','add');,'xlimmode','manual','ylimmode','manual');

    set(findobj(handles.mainaxes,'type','image'),'hitTest','off');

    set(1,'WindowKeyPressFcn',@keypressfcn);   

    

    k = waitforbuttonpress ;

    %--------------------cell removal------------------------------

    global selrow;

    tbh=findobj(1,'type','uitable');

    alldat=cell2mat(get(tbh,'userdata'));

    dat=cell2mat(get(tbh,'data'));

    conum=dat(selrow,1);

    dat=[dat(1:selrow-1,:);dat(selrow+1:end,:)];

    alldat=[alldat(1:conum-1,:);alldat(conum+1:end,:)];

    set(tbh,'data',num2cell(dat),'userData',num2cell(alldat));

    %--------------------END---------------------------------------

else

    errordlg('YOU MUST SELECT SOMETHING IN THE TABLE!');

    return

end

end

%--------------------------------------------------------------------------

function clickfcn(ar1,ar2)

global i n p;

r=get(ar1,'currentPoint');

r=r(1,1:2);

if n==0

    col='b';

else 

    col='r';

end

plot(gca,r(1),r(2),[col '*']);%text(r(1),r(2),num2str(i));

i=i+1;

p=[p,r'];

if size(p,2)>1

    line(p(1,i-2:i-1),p(2,i-2:i-1),'color',col,'linewidth',1.5);    

end

end

function keypressfcn(ar1,ar2)

if ~strcmp(ar2.Key,'space')

    return

end

global i p n ps;

per=@(p)sum(sqrt(sum(([p(:,2:end) p(:,1)]-p).^2,1)));

ntext='выделите внутренний контур, и нажмите пробел';

set(findobj(ar1,'type','uicontrol'),'string',ntext);

if size(p,2)<3

    ntext='выделите контур';

    set(findobj(ar1,'type','uicontrol'),'string',ntext);

    return

end

if n==0

    col='b';

else

    col='r';

end

line(p(1,[size(p,2) 1]),p(2,[size(p,2) 1]),'color',col,'linewidth',1.5);

if n==0

    ps=p;

    i=1;

    p=[];

    n=1;

else

    ps=flipdim(ps,2);

    p=flipdim(p,2);

    poly=discrip(ps);

    verd=true;

    for j=1:size(p,2)

        if ~poly(p(:,j))

            verd=false;

            break

        end        

    end

    if ~verd

        nntext=['красный контур (Пл: ',num2str(polyarea(p(1,:),p(2,:))),...

            ',Пер.: ' num2str(per(p)) ') не вложен в зелёный (Пл: ',...

            num2str(polyarea(ps(1,:),ps(2,:))),',Пер.: ',num2str(per(ps)) ')'];

        set(findobj(ar1,'type','uicontrol'),'string',nntext);

    else

        nntext=['красный контур (Пл: ',num2str(polyarea(p(1,:),p(2,:))),...

            ',Пер.: ' num2str(per(p)) ') вложен в зелёный (Пл: ',...

            num2str(polyarea(ps(1,:),ps(2,:))),',Пер.: ',num2str(per(ps)) ')'];

        set(findobj(ar1,'type','uicontrol'),'string',nntext);

    end

    set(findobj(ar1,'type','axes'),'buttonDownFcn',[]);

    set(ar1,'WindowKeyPressFcn',[]);

end

end

function save_data(saved_struct)

global mcount fcname;

if mcount

    save(fcname,'saved_struct','-append');

    mcount=mcount+1;

else

    original_image=get(findobj(0,'tag','imag_axes'),'userdata');

    id=num2str(sum(sum(sum(original_image))));

    cond1=0;

    for ind=1:length(dirstruct)

        if all(ismember(dirstruct(ind).name,'filecontainer'))

            cond1=cond1+1;

        end

    end

    if cond1

        fcname=['filecontainer_',id,'_',cond1,'.mat'];       

    else

        fcname=['filecontainer_',id,'.mat'];        

    end

    save(fcname,'original_image');

    mcount=1;

end

end

%--------------------------------------------------------------------------

function figure1_ResizeFcn(hObject, eventdata, handles)

tbhand=findobj(1,'type','uitable');

tab_proc_axes=findobj(1,'tag','tab_proc_axes');

tab_imag_axes=findobj(1,'tag','tab_imag_axes');

tbpos=get(tbhand,'position');

ex=get(tbhand,'extent');

tbpos(3)=ex(3);%+.028;

set(tbhand,'position',tbpos);

hspan=((1-sum(tbpos([1 3]))-2*.05)-.05)/2;

tpappos=get(tab_proc_axes,'position');

tpappos(1)=sum(tbpos([1 3]))+.05 ;

tpappos(3)=hspan;

set(tab_proc_axes,'position',tpappos);

tiappos=get(tab_imag_axes,'position');

tiappos(1)=sum(tpappos([1 3]))+.05 ;

tiappos(3)=hspan;

set(tab_imag_axes,'position',tiappos);

%----------------------------------------------

ed1=findobj(1,'tag','ed1');

ed2=findobj(1,'tag','ed2');

ed1_pos=[sum(tbpos([1,3]))+.05 .05 .1 .05];

set(ed1,'position',ed1_pos); 

ed2_pos=[sum(ed1_pos([1,3]))+.05 .05 .1 .05];

set(ed2,'position',ed2_pos); 

end

Dataset Files

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Documentation

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[1] Alexander Notchenko, Oleg Gradov, "WSG_v.1.05 software for neural structure morphometry, including on-chip mapping", IEEE Dataport, 2019. [Online]. Available: http://dx.doi.org/10.21227/fnrx-3t19. Accessed: Aug. 21, 2019.
@data{fnrx-3t19-19,
doi = {10.21227/fnrx-3t19},
url = {http://dx.doi.org/10.21227/fnrx-3t19},
author = {Alexander Notchenko; Oleg Gradov },
publisher = {IEEE Dataport},
title = {WSG_v.1.05 software for neural structure morphometry, including on-chip mapping},
year = {2019} }
TY - DATA
T1 - WSG_v.1.05 software for neural structure morphometry, including on-chip mapping
AU - Alexander Notchenko; Oleg Gradov
PY - 2019
PB - IEEE Dataport
UR - 10.21227/fnrx-3t19
ER -
Alexander Notchenko, Oleg Gradov. (2019). WSG_v.1.05 software for neural structure morphometry, including on-chip mapping. IEEE Dataport. http://dx.doi.org/10.21227/fnrx-3t19
Alexander Notchenko, Oleg Gradov, 2019. WSG_v.1.05 software for neural structure morphometry, including on-chip mapping. Available at: http://dx.doi.org/10.21227/fnrx-3t19.
Alexander Notchenko, Oleg Gradov. (2019). "WSG_v.1.05 software for neural structure morphometry, including on-chip mapping." Web.
1. Alexander Notchenko, Oleg Gradov. WSG_v.1.05 software for neural structure morphometry, including on-chip mapping [Internet]. IEEE Dataport; 2019. Available from : http://dx.doi.org/10.21227/fnrx-3t19
Alexander Notchenko, Oleg Gradov. "WSG_v.1.05 software for neural structure morphometry, including on-chip mapping." doi: 10.21227/fnrx-3t19