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neuropixels_trajectory_explorer_rat.m
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%% Neuropixels Trajector Explorer
% neuropixels_trajectory_explorer
% Andy Peters (peters.andrew.j@gmail.com)
%
% GUI for planning Neuropixels trajectories with the Allen CCF atlas
%
% Instructions for use:
% https://github.com/petersaj/neuropixels_trajectory_explorer
%% GUI setup
function neuropixels_trajectory_explorer_rat
% Check MATLAB version
matlab_version = version('-date');
if str2num(matlab_version(end-3:end)) <= 2016
error('Old MATLAB - allen_ccf_npx requires 2016 or later');
end
% Check for dependencies
% (npy-matlab to load in atlas)
if ~exist('readNPY','file')
error('"npy-matlab" code not found, download here and add to matlab path: https://github.com/kwikteam/npy-matlab')
end
% Initialize gui_data structure
gui_data = struct;
% ~~~~ Load atlas and associated data
% Load in atlas
% Find path with ratlas
atlas_path = fileparts(which('WHS_SD_rat_T2star_v1.01.nii.gz'));
if isempty(atlas_path)
error('Rat atlas not in MATLAB path (click ''Set path'', add folder with CCF)');
end
% Load ratlas
tv = cast(rescale(permute(niftiread(fullfile(atlas_path,'WHS_SD_rat_T2star_v1.01.nii.gz')),[2,3,1]),0,255),'uint8');
av = permute(niftiread(fullfile(atlas_path,'WHS_SD_rat_atlas_v4.nii.gz')),[2,3,1]);
% (zero tv where av not defined)
tv(av == 0) = 0;
% Load labels (made from auto-generated script)
filename = 'C:\Users\Andrew\OneDrive for Business\Documents\Atlases\WHSrat\WHS_SD_rat_atlas_v4.label';
startRow = 15;
formatSpec = '%5f%6f%5f%5f%9f%3f%3f%s%[^\n\r]';
fileID = fopen(filename,'r');
dataArray = textscan(fileID, formatSpec, 'Delimiter', '', 'WhiteSpace', '', 'TextType', 'string', 'HeaderLines' ,startRow-1, 'ReturnOnError', false, 'EndOfLine', '\r\n');
dataArray{8} = strtrim(dataArray{8});
fclose(fileID);
st_raw = table(dataArray{1:end-1}, 'VariableNames', {'index','R','G','B','A','VIS','MSH','safe_name'});
st = table;
st(st_raw.index(2:end),:) = st_raw(2:end,:);
clearvars filename startRow formatSpec fileID dataArray ans;
% Create colormap
ccf_cmap = [st.R,st.G,st.B]/255;
% ~~~~ Make transform matrix from CCF to bregma/mm coordinates
% This is in the coordinates pdf
bregma_ccf = [635,440,246]; % [AP,DV,ML]
ccf_translation_tform = eye(4)+[zeros(3,4);-bregma_ccf([3,1,2]),0];
% (scale voxel to mm)
voxel2mm = 0.039;
scale = voxel2mm./[-1,1,-1]; % [AP,ML,DV]
ccf_scale_tform = eye(4).*[scale,1]';
ccf_bregma_tform_matrix = ccf_translation_tform*ccf_scale_tform;
ccf_bregma_tform = affine3d(ccf_bregma_tform_matrix);
% ~~~~ Make GUI axes and objects
% Set up the gui
probe_atlas_gui = figure('Toolbar','none','Menubar','none','color','w', ...
'Name','Neuropixels Trajectory Explorer (Rat)','Units','normalized','Position',[0.21,0.2,0.7,0.7]);
% Set up the atlas axes
axes_atlas = axes('Position',[-0.3,0.1,1.2,0.8],'ZDir','reverse');
axis(axes_atlas,'vis3d','equal','off','manual'); hold(axes_atlas,'on');
% Draw brain outline
slice_spacing = 5;
brain_volume = ...
bwmorph3(bwmorph3(av(1:slice_spacing:end, ...
1:slice_spacing:end,1:slice_spacing:end)>1,'majority'),'majority');
[ap_grid_ccf,dv_grid_ccf,ml_grid_ccf] = ...
ndgrid(1:slice_spacing:size(av,1), ...
1:slice_spacing:size(av,2), ...
1:slice_spacing:size(av,3));
[ml_grid_bregma,ap_grid_bregma,dv_grid_bregma] = ...
transformPointsForward(ccf_bregma_tform,ml_grid_ccf,ap_grid_ccf,dv_grid_ccf);
brain_outline_patchdata = reducepatch(isosurface(ml_grid_bregma,ap_grid_bregma, ...
dv_grid_bregma,brain_volume,0.5),0.1);
brain_outline = patch( ...
'Vertices',brain_outline_patchdata.vertices, ...
'Faces',brain_outline_patchdata.faces, ...
'FaceColor',[0.5,0.5,0.5],'EdgeColor','none','FaceAlpha',0.1);
view([30,150]);
caxis([1,size(ccf_cmap,1)]);
xlim(prctile(ml_grid_bregma(:),[0,100]));
ylim(prctile(ap_grid_bregma(:),[0,100]));
zlim(prctile(dv_grid_bregma(:),[0,100]));
grid on;
% Set up the probe reference/actual
probe_ref_top = [0,0,-0.1];
probe_ref_bottom = [0,0,prctile(dv_grid_bregma(:),100)];
probe_ref_vector = [probe_ref_top',probe_ref_bottom'];
probe_ref_line = line(probe_ref_vector(1,:),probe_ref_vector(2,:),probe_ref_vector(3,:), ...
'linewidth',1.5,'color','r','linestyle','--');
probe_length = 3.840; % IMEC phase 3 (in mm)
probe_vector = [probe_ref_vector(:,1),diff(probe_ref_vector,[],2)./ ...
norm(diff(probe_ref_vector,[],2))*probe_length + probe_ref_vector(:,1)];
probe_line = line(probe_vector(1,:),probe_vector(2,:),probe_vector(3,:), ...
'linewidth',3,'color','b','linestyle','-');
% Set up the text to display coordinates
probe_coordinates_text = uicontrol('Style','text','String','', ...
'Units','normalized','Position',[0,0.9,0.5,0.1], ...
'BackgroundColor','w','HorizontalAlignment','left','FontSize',12);
% Set up the probe area axes
axes_probe_areas = axes('Position',[0.7,0.1,0.03,0.8]);
set(axes_probe_areas,'FontSize',11);
yyaxis(axes_probe_areas,'left');
probe_areas_plot = imagesc(0);
set(axes_probe_areas,'XTick','','YLim',[0,probe_length],'YColor','k','YDir','reverse');
ylabel(axes_probe_areas,'Depth (mm)');
yyaxis(axes_probe_areas,'right');
set(axes_probe_areas,'XTick','','YLim',[0,probe_length],'YColor','k','YDir','reverse');
title(axes_probe_areas,'Probe areas');
caxis(axes_probe_areas,[1,size(ccf_cmap,1)]);
colormap(axes_probe_areas,ccf_cmap);
% Store data
gui_data.tv = tv; % Intensity atlas
gui_data.av = av; % Annotated atlas
gui_data.st = st; % Labels table
gui_data.cmap = ccf_cmap; % Atlas colormap
gui_data.ccf_bregma_tform = ccf_bregma_tform;
gui_data.probe_length = probe_length; % Length of probe
gui_data.structure_plot_idx = []; % Plotted structures
gui_data.probe_angle = [0;90]; % Probe angles in ML/DV
%Store handles
gui_data.handles.cortex_outline = brain_outline;
gui_data.handles.structure_patch = []; % Plotted structures
gui_data.handles.axes_atlas = axes_atlas; % Axes with 3D atlas
gui_data.handles.axes_probe_areas = axes_probe_areas; % Axes with probe areas
gui_data.handles.slice_plot = surface(axes_atlas,'EdgeColor','none'); % Slice on 3D atlas
gui_data.handles.slice_volume = 'tv'; % The volume shown in the slice
gui_data.handles.probe_ref_line = probe_ref_line; % Probe reference line on 3D atlas
gui_data.handles.probe_line = probe_line; % Probe reference line on 3D atlas
gui_data.handles.probe_areas_plot = probe_areas_plot; % Color-coded probe regions
gui_data.probe_coordinates_text = probe_coordinates_text; % Probe coordinates text
% Make 3D rotation the default state (toggle on/off with 'r')
h = rotate3d(axes_atlas);
h.Enable = 'on';
% Update the slice whenever a rotation is completed
h.ActionPostCallback = @update_slice;
% Set functions for key presses
hManager = uigetmodemanager(probe_atlas_gui);
[hManager.WindowListenerHandles.Enabled] = deal(false);
set(probe_atlas_gui,'KeyPressFcn',@key_press);
set(probe_atlas_gui,'KeyReleaseFcn',@key_release);
% Upload gui_data
guidata(probe_atlas_gui, gui_data);
% Display the first slice and update the probe position
update_slice(probe_atlas_gui);
update_probe_coordinates(probe_atlas_gui);
%% Buttons
button_fontsize = 12;
%%% View angle buttons
view_button_position = [0,0,0.05,0.05];
clear view_button_h
view_button_h(1) = uicontrol('Parent',probe_atlas_gui,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',view_button_position,'String','Coronal','Callback',{@view_coronal,probe_atlas_gui});
view_button_h(end+1) = uicontrol('Parent',probe_atlas_gui,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',view_button_position,'String','Sagittal','Callback',{@view_sagittal,probe_atlas_gui});
view_button_h(end+1) = uicontrol('Parent',probe_atlas_gui,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',view_button_position,'String','Horizontal','Callback',{@view_horizontal,probe_atlas_gui});
align(view_button_h,'fixed',0.1,'middle');
%%% Control panel
control_panel = figure('Toolbar','none','Menubar','none','color','w', ...
'Name','Controls','Units','normalized','Position',[0.09,0.2,0.11,0.7]);
button_position = [0.05,0.05,0.9,0.05];
header_text_position = [0.05,0.05,0.9,0.03];
clear controls_h
% (probe controls)
controls_h(1) = uicontrol('Parent',control_panel,'Style','text','FontSize',button_fontsize, ...
'Units','normalized','Position',header_text_position,'String','Probe controls:', ...
'BackgroundColor','w','FontWeight','bold');
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','text','FontSize',button_fontsize, ...
'Units','normalized','Position',header_text_position,'String','Whole probe: arrow keys', ...
'BackgroundColor','w');
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','text','FontSize',button_fontsize, ...
'Units','normalized','Position',header_text_position,'String','Depth: alt+arrow keys', ...
'BackgroundColor','w');
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','text','FontSize',button_fontsize, ...
'Units','normalized','Position',header_text_position,'String','Probe tip: shift+arrow keys', ...
'BackgroundColor','w');
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','text','FontSize',button_fontsize, ...
'Units','normalized','Position',header_text_position,'String','(changes probe angle)', ...
'BackgroundColor','w');
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Set entry','Callback',{@set_probe_entry,probe_atlas_gui});
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Set endpoint','Callback',{@set_probe_endpoint,probe_atlas_gui});
% (area selector)
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','text','FontSize',button_fontsize, ...
'Units','normalized','Position',header_text_position,'String','3D areas:', ...
'BackgroundColor','w','FontWeight','bold');
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','List areas','Callback',{@add_area_list,probe_atlas_gui});
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Search areas','Callback',{@add_area_search,probe_atlas_gui});
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Remove areas','Callback',{@remove_area,probe_atlas_gui});
% (visibility toggle)
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','text','FontSize',button_fontsize, ...
'Units','normalized','Position',header_text_position,'String','Toggle visibility:', ...
'BackgroundColor','w','FontWeight','bold');
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Slice','Callback',{@visibility_slice,probe_atlas_gui});
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Brain outline','Callback',{@visibility_brain_outline,probe_atlas_gui});
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Grid','Callback',{@visibility_grid,probe_atlas_gui});
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Probe','Callback',{@visibility_probe,probe_atlas_gui});
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','3D areas','Callback',{@visibility_3d_areas,probe_atlas_gui});
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Dark mode','Callback',{@visibility_darkmode,probe_atlas_gui});
% (other)
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','text','FontSize',button_fontsize, ...
'Units','normalized','Position',header_text_position,'String','Other:', ...
'BackgroundColor','w','FontWeight','bold');
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Export coordinates','Callback',{@export_coordinates,probe_atlas_gui});
controls_h(end+1) = uicontrol('Parent',control_panel,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',button_position,'String','Load/plot histology','Callback',{@probe_histology,probe_atlas_gui});
set(controls_h(1),'Position',header_text_position+[0,0.9,0,0]);
align(fliplr(controls_h),'center','distribute');
% Set close functions for windows
set(probe_atlas_gui,'CloseRequestFcn',{@gui_close,probe_atlas_gui,control_panel});
set(control_panel,'CloseRequestFcn',{@gui_close,probe_atlas_gui,control_panel});
end
function gui_close(h,eventdata,probe_atlas_gui,control_panel)
% When closing either GUI or control panel, close both windows
delete(control_panel);
delete(probe_atlas_gui);
end
%% Probe controls and slice updating
function key_press(probe_atlas_gui,eventdata)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Set step size in millimeters
step_size = 0.1;
% Update probe coordinates
ap_offset = 0;
ml_offset = 0;
probe_offset = 0;
angle_change = [0;0];
switch eventdata.Key
case 'uparrow'
if isempty(eventdata.Modifier)
ap_offset = step_size;
elseif any(strcmp(eventdata.Modifier,'shift'))
angle_change = [0;step_size];
elseif any(strcmp(eventdata.Modifier,'alt'))
probe_offset = -step_size;
end
case 'downarrow'
if isempty(eventdata.Modifier)
ap_offset = -step_size;
elseif any(strcmp(eventdata.Modifier,'shift'))
angle_change = [0;-step_size];
elseif any(strcmp(eventdata.Modifier,'alt'))
probe_offset = step_size;
end
case 'leftarrow'
if isempty(eventdata.Modifier)
ml_offset = -step_size;
elseif any(strcmp(eventdata.Modifier,'shift'))
angle_change = [-step_size;0];
end
case 'rightarrow'
if isempty(eventdata.Modifier)
ml_offset = step_size;
elseif any(strcmp(eventdata.Modifier,'shift'))
angle_change = [step_size;0];
end
end
% Draw updated probe
if any([ap_offset,ml_offset,probe_offset])
% (AP/ML)
set(gui_data.handles.probe_ref_line,'XData',get(gui_data.handles.probe_ref_line,'XData') + ml_offset);
set(gui_data.handles.probe_line,'XData',get(gui_data.handles.probe_line,'XData') + ml_offset);
set(gui_data.handles.probe_ref_line,'YData',get(gui_data.handles.probe_ref_line,'YData') + ap_offset);
set(gui_data.handles.probe_line,'YData',get(gui_data.handles.probe_line,'YData') + ap_offset);
% (probe axis)
old_probe_vector = cell2mat(get(gui_data.handles.probe_line,{'XData','YData','ZData'})');
move_probe_vector = diff(old_probe_vector,[],2)./ ...
norm(diff(old_probe_vector,[],2))*probe_offset;
new_probe_vector = bsxfun(@plus,old_probe_vector,move_probe_vector);
set(gui_data.handles.probe_line,'XData',new_probe_vector(1,:), ...
'YData',new_probe_vector(2,:),'ZData',new_probe_vector(3,:));
end
% (angle)
if any(angle_change)
gui_data = update_probe_angle(probe_atlas_gui,angle_change);
end
% Upload gui_data
guidata(probe_atlas_gui, gui_data);
end
function key_release(probe_atlas_gui,eventdata)
% Get guidata
gui_data = guidata(probe_atlas_gui);
switch eventdata.Key
case {'rightarrow','leftarrow','uparrow','downarrow'}
% Update the probe info/slice on arrow release
update_probe_coordinates(probe_atlas_gui);
update_slice(probe_atlas_gui);
end
% Upload gui_data
guidata(probe_atlas_gui, gui_data);
end
function update_slice(probe_atlas_gui,varargin)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Only update the slice if it's visible
if strcmp(gui_data.handles.slice_plot(1).Visible,'on')
% Get current position of camera
curr_campos = campos(gui_data.handles.axes_atlas);
% Get probe vector
probe_ref_top = [gui_data.handles.probe_ref_line.XData(1), ...
gui_data.handles.probe_ref_line.YData(1),gui_data.handles.probe_ref_line.ZData(1)];
probe_ref_bottom = [gui_data.handles.probe_ref_line.XData(2), ...
gui_data.handles.probe_ref_line.YData(2),gui_data.handles.probe_ref_line.ZData(2)];
probe_vector = probe_ref_top - probe_ref_bottom;
% Get probe-camera vector
probe_camera_vector = probe_ref_top - curr_campos;
% Get the vector to plot the plane in (along with probe vector)
plot_vector = cross(probe_camera_vector,probe_vector);
% Get the normal vector of the plane
normal_vector = cross(plot_vector,probe_vector);
% Get the plane offset through the probe
plane_offset = -(normal_vector*probe_ref_top');
% Define a plane of points to index
% (the plane grid is defined based on the which cardinal plan is most
% orthogonal to the plotted plane. this is janky but it works)
ml_lim = xlim(gui_data.handles.axes_atlas);
ap_lim = ylim(gui_data.handles.axes_atlas);
dv_lim = zlim(gui_data.handles.axes_atlas);
slice_px_space = 0.05; % resolution of slice to grab
[~,cam_plane] = max(abs(normal_vector./norm(normal_vector)));
switch cam_plane
case 1
[plane_ap_bregma,plane_dv_bregma] = ndgrid(...
ap_lim(1):slice_px_space:ap_lim(2),...
dv_lim(1):slice_px_space:dv_lim(2));
plane_ml_bregma = ...
(normal_vector(2)*plane_ap_bregma+normal_vector(3)*plane_dv_bregma + plane_offset)/ ...
-normal_vector(1);
case 2
[plane_ml_bregma,plane_dv_bregma] = ndgrid(...
ml_lim(1):slice_px_space:ml_lim(2),...
dv_lim(1):slice_px_space:dv_lim(2));
plane_ap_bregma = ...
(normal_vector(3)*plane_dv_bregma+normal_vector(1)*plane_ml_bregma + plane_offset)/ ...
-normal_vector(2);
case 3
[plane_ml_bregma,plane_ap_bregma] = ndgrid(...
ml_lim(1):slice_px_space:ml_lim(2),...
ap_lim(1):slice_px_space:ap_lim(2));
plane_dv_bregma = ...
(normal_vector(2)*plane_ap_bregma+normal_vector(1)*plane_ml_bregma + plane_offset)/ ...
-normal_vector(3);
end
% Transform bregma coordinates to CCF coordinates
[plane_ml_ccf,plane_ap_ccf,plane_dv_ccf] = ...
transformPointsInverse(gui_data.ccf_bregma_tform,plane_ml_bregma,plane_ap_bregma,plane_dv_bregma);
% Grab pixels from (selected) volume
atlas_downsample = 3; % (downsample atlas to make this faster)
switch gui_data.handles.slice_volume
case 'tv'
curr_slice = single(interpn( ...
imresize3(gui_data.tv,1/atlas_downsample,'nearest'), ...
plane_ap_ccf/atlas_downsample, ...
plane_dv_ccf/atlas_downsample, ...
plane_ml_ccf/atlas_downsample,'nearest'));
curr_slice(curr_slice < 20) = NaN; % threshold values
colormap(gui_data.handles.axes_atlas,'gray');
caxis(gui_data.handles.axes_atlas,[0,255]);
case 'av'
curr_slice = single(interpn( ...
imresize3(gui_data.av,1/atlas_downsample,'nearest'), ...
plane_ap_ccf/atlas_downsample, ...
plane_dv_ccf/atlas_downsample, ...
plane_ml_ccf/atlas_downsample,'nearest'));
curr_slice(curr_slice <= 1) = NaN;
colormap(gui_data.handles.axes_atlas,gui_data.cmap);
caxis(gui_data.handles.axes_atlas,[1,size(gui_data.cmap,1)]);
end
% Update the slice display
set(gui_data.handles.slice_plot, ...
'XData',plane_ml_bregma,'YData',plane_ap_bregma,'ZData',plane_dv_bregma,'CData',curr_slice);
% Upload gui_data
guidata(probe_atlas_gui, gui_data);
end
end
function set_probe_entry(h,eventdata,probe_atlas_gui)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Prompt for angles
prompt_text = { ...
'AP position (mm from bregma)', ...
'ML position (mm from bregma)', ...
'Azimuth angle (relative to lambda -> bregma)', ....
'Elevation angle (relative to horizontal)'};
new_probe_position_input = inputdlg(prompt_text,'Set probe position',1);
if any(cellfun(@isempty,new_probe_position_input))
error('Not all coordinates entered');
end
new_probe_position = cellfun(@str2num,new_probe_position_input);
% Convert degrees to radians
probe_angle_rad = (new_probe_position(3:4)/360)*2*pi;
% Update the probe and trajectory reference
ml_lim = xlim(gui_data.handles.axes_atlas);
ap_lim = ylim(gui_data.handles.axes_atlas);
dv_lim = zlim(gui_data.handles.axes_atlas);
max_ref_length = norm([range(ap_lim);range(dv_lim);range(ml_lim)]);
[y,x,z] = sph2cart(pi-probe_angle_rad(1),pi-probe_angle_rad(2),max_ref_length);
% Get top of probe reference with user brain intersection point
% (get DV location of brain surface at chosen ML/AP point)
dv_query_bregma = interp1([0,1], ...
[new_probe_position([2,1])',-1; ...
new_probe_position([2,1])',6],linspace(0,1,100));
[ml_query_ccf,ap_query_ccf,dv_query_ccf] = ...
transformPointsInverse(gui_data.ccf_bregma_tform, ...
dv_query_bregma(:,1),dv_query_bregma(:,2),dv_query_bregma(:,3));
atlas_downsample = 5;
dv_ccf_line = interpn( ...
imresize3(gui_data.av,1/atlas_downsample,'nearest'), ...
ap_query_ccf/atlas_downsample, ...
dv_query_ccf/atlas_downsample, ...
ml_query_ccf/atlas_downsample,'nearest');
dv_brain_intersect_idx = find(dv_ccf_line > 1,1);
probe_brain_dv = dv_query_bregma(dv_brain_intersect_idx,3);
% (back up to 0 DV in CCF space)
probe_ref_top_ap = interp1(probe_brain_dv+[0,z],new_probe_position(1)+[0,y],0,'linear','extrap');
probe_ref_top_ml = interp1(probe_brain_dv+[0,z],new_probe_position(2)+[0,x],0,'linear','extrap');
% Set new probe position
probe_ref_top = [probe_ref_top_ml,probe_ref_top_ap,0];
probe_ref_bottom = probe_ref_top + [x,y,z];
probe_ref_vector = [probe_ref_top;probe_ref_bottom]';
set(gui_data.handles.probe_ref_line,'XData',probe_ref_vector(1,:), ...
'YData',probe_ref_vector(2,:), ...
'ZData',probe_ref_vector(3,:));
probe_vector = [probe_ref_vector(:,1),diff(probe_ref_vector,[],2)./ ...
norm(diff(probe_ref_vector,[],2))*gui_data.probe_length + probe_ref_vector(:,1)];
set(gui_data.handles.probe_line,'XData',probe_vector(1,:), ...
'YData',probe_vector(2,:),'ZData',probe_vector(3,:));
% Upload gui_data
gui_data.probe_angle = (probe_angle_rad/(2*pi))*360;
guidata(probe_atlas_gui, gui_data);
% Update the slice and probe coordinates
update_slice(probe_atlas_gui);
update_probe_coordinates(probe_atlas_gui);
end
function set_probe_endpoint(h,eventdata,probe_atlas_gui)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Prompt for angles
prompt_text = { ...
'AP position (mm from bregma)', ...
'ML position (mm from bregma)', ...
'DV position (mm from bregma)', ...
'Azimuth angle (relative to lambda -> bregma)', ....
'Elevation angle (relative to horizontal)'};
new_probe_position_input = inputdlg(prompt_text,'Set probe position',1);
if any(cellfun(@isempty,new_probe_position_input))
error('Not all coordinates entered');
end
new_probe_position = cellfun(@str2num,new_probe_position_input);
% Convert degrees to radians
probe_angle_rad = (new_probe_position(4:5)/360)*2*pi;
% Update the probe and trajectory reference
max_ref_length = norm([max(gui_data.ap_coords);max(gui_data.dv_coords);max(gui_data.ml_coords)]);
[y,x,z] = sph2cart(pi-probe_angle_rad(1),pi-probe_angle_rad(2),max_ref_length);
% Move probe reference (draw line through point and DV 0 with max length)
probe_ref_top_ap = interp1(new_probe_position(3)+[0,z],new_probe_position(1)+[0,y],0,'linear','extrap');
probe_ref_top_ml = interp1(new_probe_position(3)+[0,z],new_probe_position(2)+[0,x],0,'linear','extrap');
probe_ref_top = [probe_ref_top_ml,probe_ref_top_ap,0];
probe_ref_bottom = probe_ref_top + [x,y,z];
probe_ref_vector = [probe_ref_top;probe_ref_bottom]';
set(gui_data.handles.probe_ref_line,'XData',probe_ref_vector(1,:), ...
'YData',probe_ref_vector(2,:), ...
'ZData',probe_ref_vector(3,:));
% Move probe (lock endpoint, back up length of probe)
probe_vector = [diff(probe_ref_vector,[],2)./norm(diff(probe_ref_vector,[],2))* ...
-gui_data.probe_length + new_probe_position([2,1,3]), ...
new_probe_position([2,1,3])];
set(gui_data.handles.probe_line,'XData',probe_vector(1,:), ...
'YData',probe_vector(2,:),'ZData',probe_vector(3,:));
% Upload gui_data
gui_data.probe_angle = (probe_angle_rad/(2*pi))*360;
guidata(probe_atlas_gui, gui_data);
% Update the slice and probe coordinates
update_slice(probe_atlas_gui);
update_probe_coordinates(probe_atlas_gui);
end
function gui_data = update_probe_angle(probe_atlas_gui,angle_change)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Get the positions of the probe and trajectory reference
probe_ref_vector = cell2mat(get(gui_data.handles.probe_ref_line,{'XData','YData','ZData'})');
probe_vector = cell2mat(get(gui_data.handles.probe_line,{'XData','YData','ZData'})');
% Update the probe trajectory reference angle
% % (Old, unused: spherical/manipulator coordinates)
% % Set new angle
% new_angle = gui_data.probe_angle + angle_change;
% gui_data.probe_angle = new_angle;
%
% [ap_max,dv_max,ml_max] = size(gui_data.tv);
%
% max_ref_length = sqrt(sum(([ap_max,dv_max,ml_max].^2)));
%
% probe_angle_rad = (gui_data.probe_angle./360)*2*pi;
% [x,y,z] = sph2cart(pi-probe_angle_rad(1),probe_angle_rad(2),max_ref_length);
%
% new_probe_ref_top = [probe_ref_vector(1,1),probe_ref_vector(2,1),0];
% new_probe_ref_bottom = new_probe_ref_top + [x,y,z];
% new_probe_ref_vector = [new_probe_ref_top;new_probe_ref_bottom]';
% (New: cartesian coordinates of the trajectory bottom)
new_probe_ref_vector = [probe_ref_vector(:,1), ...
probe_ref_vector(:,2) + [angle_change;0]];
% (calculate angle with flipped x/y and -y to make zero be forward midline)
[probe_azimuth,probe_elevation] = cart2sph( ...
diff(fliplr(-new_probe_ref_vector(2,:))), ...
diff(fliplr(new_probe_ref_vector(1,:))), ...
diff(fliplr(-new_probe_ref_vector(3,:))));
gui_data.probe_angle = [probe_azimuth,probe_elevation]*(360/(2*pi));
set(gui_data.handles.probe_ref_line,'XData',new_probe_ref_vector(1,:), ...
'YData',new_probe_ref_vector(2,:), ...
'ZData',new_probe_ref_vector(3,:));
% Update probe (retain depth)
new_probe_vector = [new_probe_ref_vector(:,1),diff(new_probe_ref_vector,[],2)./ ...
norm(diff(new_probe_ref_vector,[],2))*gui_data.probe_length + new_probe_ref_vector(:,1)];
probe_depth = sqrt(sum((probe_ref_vector(:,1) - probe_vector(:,1)).^2));
new_probe_vector_depth = (diff(new_probe_vector,[],2)./ ...
norm(diff(new_probe_vector,[],2))*probe_depth) + new_probe_vector;
set(gui_data.handles.probe_line,'XData',new_probe_vector_depth(1,:), ...
'YData',new_probe_vector_depth(2,:),'ZData',new_probe_vector_depth(3,:));
% Upload gui_data
guidata(probe_atlas_gui, gui_data);
end
function update_probe_coordinates(probe_atlas_gui,varargin)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Get the positions of the probe and trajectory reference
probe_ref_vector = cell2mat(get(gui_data.handles.probe_ref_line,{'XData','YData','ZData'})');
probe_vector = cell2mat(get(gui_data.handles.probe_line,{'XData','YData','ZData'})');
trajectory_n_coords = max(abs(diff(probe_ref_vector,[],2)))*1000; % 1um resolution
[trajectory_ml_coords_bregma,trajectory_ap_coords_bregma,trajectory_dv_coords_bregma] = deal( ...
linspace(probe_ref_vector(1,1),probe_ref_vector(1,2),trajectory_n_coords), ...
linspace(probe_ref_vector(2,1),probe_ref_vector(2,2),trajectory_n_coords), ...
linspace(probe_ref_vector(3,1),probe_ref_vector(3,2),trajectory_n_coords));
probe_n_coords = sqrt(sum(diff(probe_vector,[],2).^2))*1000; % 1um resolution along active sites
probe_coords_depth = linspace(0,gui_data.probe_length,probe_n_coords);
[probe_ml_coords_bregma,probe_ap_coords_bregma,probe_dv_coords_bregma] = deal( ...
linspace(probe_vector(1,1),probe_vector(1,2),probe_n_coords), ...
linspace(probe_vector(2,1),probe_vector(2,2),probe_n_coords), ...
linspace(probe_vector(3,1),probe_vector(3,2),probe_n_coords));
% Transform bregma coordinates to CCF coordinates
[trajectory_ml_coords_ccf,trajectory_ap_coords_ccf,trajectory_dv_coords_ccf] = ...
transformPointsInverse(gui_data.ccf_bregma_tform, ...
trajectory_ml_coords_bregma,trajectory_ap_coords_bregma,trajectory_dv_coords_bregma);
[probe_ml_coords_ccf,probe_ap_coords_ccf,probe_dv_coords_ccf] = ...
transformPointsInverse(gui_data.ccf_bregma_tform, ...
probe_ml_coords_bregma,probe_ap_coords_bregma,probe_dv_coords_bregma);
% Get brain labels across the probe and trajectory, and intersection with brain
atlas_downsample = 3; % (downsample atlas to make this faster)
trajectory_areas = interpn( ...
imresize3(gui_data.av,1/atlas_downsample,'nearest'), ...
trajectory_ap_coords_ccf/atlas_downsample, ...
trajectory_dv_coords_ccf/atlas_downsample, ...
trajectory_ml_coords_ccf/atlas_downsample,'nearest');
trajectory_brain_idx = find(trajectory_areas > 1,1);
trajectory_brain_intersect = ...
[trajectory_ml_coords_bregma(trajectory_brain_idx), ...
trajectory_ap_coords_bregma(trajectory_brain_idx), ...
trajectory_dv_coords_bregma(trajectory_brain_idx)]';
% (if the probe doesn't intersect the brain, don't update)
if isempty(trajectory_brain_intersect)
return
end
probe_areas = interpn( ...
imresize3(gui_data.av,1/atlas_downsample,'nearest'), ...
probe_ap_coords_ccf/atlas_downsample, ...
probe_dv_coords_ccf/atlas_downsample, ...
probe_ml_coords_ccf/atlas_downsample,'nearest')';
probe_areas(probe_areas == 0) = 1; % set 0's (out of CCF) to 1's (non-brain)
probe_area_boundaries = intersect(unique([find(~isnan(probe_areas),1,'first'); ...
find(diff(probe_areas) ~= 0);find(~isnan(probe_areas),1,'last')]),find(~isnan(probe_areas)));
probe_area_centers_idx = round(probe_area_boundaries(1:end-1) + diff(probe_area_boundaries)/2);
probe_area_centers = probe_coords_depth(probe_area_centers_idx);
probe_area_labels = gui_data.st.safe_name(probe_areas(probe_area_centers_idx));
% Get coordinate from bregma and probe-axis depth from surface
% (round to nearest 10 microns)
probe_bregma_coordinate = trajectory_brain_intersect(1:2);
probe_depth = norm(trajectory_brain_intersect - probe_vector(:,2));
% Update the text
probe_angle_text = sprintf('Probe angle: %.0f%c azimuth, %.0f%c elevation', ...
gui_data.probe_angle(1),char(176),gui_data.probe_angle(2),char(176));
probe_insertion_text = sprintf('Probe insertion (mm from bregma): %.2f AP, %.2f ML, %.2f Probe-axis', ...
probe_bregma_coordinate(2),probe_bregma_coordinate(1),probe_depth);
probe_endpoint_text = sprintf('(Probe endpoint (mm from bregma): %.2f AP, %.2f ML, %.2f DV)', ...
probe_vector(2,2),probe_vector(1,2),probe_vector(3,2));
probe_text = {probe_angle_text,probe_insertion_text,probe_endpoint_text};
set(gui_data.probe_coordinates_text,'String',probe_text);
% Update the probe areas
yyaxis(gui_data.handles.axes_probe_areas,'right');
set(gui_data.handles.probe_areas_plot,'YData',probe_coords_depth,'CData',probe_areas);
set(gui_data.handles.axes_probe_areas,'YTick',probe_area_centers,'YTickLabels',probe_area_labels);
yyaxis(gui_data.handles.axes_probe_areas,'left');
caxis(gui_data.handles.axes_probe_areas,[1,size(gui_data.cmap,1)]);
% Upload gui_data
guidata(probe_atlas_gui, gui_data);
end
%% Button functions
function view_coronal(h,eventdata,probe_atlas_gui)
% Set coronal view
gui_data = guidata(probe_atlas_gui);
view(gui_data.handles.axes_atlas,[0,0]);
update_slice(probe_atlas_gui);
end
function view_sagittal(h,eventdata,probe_atlas_gui)
% Set sagittal view
gui_data = guidata(probe_atlas_gui);
view(gui_data.handles.axes_atlas,[-90,0]);
update_slice(probe_atlas_gui);
end
function view_horizontal(h,eventdata,probe_atlas_gui)
% Set horizontal view
gui_data = guidata(probe_atlas_gui);
view(gui_data.handles.axes_atlas,[0,90]);
update_slice(probe_atlas_gui);
end
function add_area_list(h,eventdata,probe_atlas_gui)
% List all CCF areas, draw selected
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Prompt for which structures to show (only structures which are
% labelled in the slice-spacing downsampled annotated volume)
slice_spacing = 10;
parsed_structures = setdiff(unique(reshape(gui_data.av(1:slice_spacing:end, ...
1:slice_spacing:end,1:slice_spacing:end),[],1)),0);
plot_structure_parsed = listdlg('PromptString','Select a structure to plot:', ...
'ListString',gui_data.st.safe_name(parsed_structures),'ListSize',[520,500], ...
'SelectionMode','single');
plot_structure = parsed_structures(plot_structure_parsed);
% (change: show all structures even if not parsed to allow hierarchy)
plot_structure = listdlg('PromptString','Select a structure to plot:', ...
'ListString',gui_data.st.safe_name,'ListSize',[520,500], ...
'SelectionMode','single');
% Draw areas
draw_areas(probe_atlas_gui,slice_spacing,plot_structure);
end
function add_area_search(h,eventdata,probe_atlas_gui)
% Search all CCF areas, draw selected
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Prompt for which structures to show (only structures which are
% labelled in the slice-spacing downsampled annotated volume)
slice_spacing = 10;
parsed_structures = unique(reshape(gui_data.av(1:slice_spacing:end, ...
1:slice_spacing:end,1:slice_spacing:end),[],1));
structure_search = lower(inputdlg('Search structures'));
structure_match = find(contains(lower(gui_data.st.safe_name),structure_search));
% list_structures = intersect(parsed_structures,structure_match);
% (change: show all structures even if not parsed to allow hierarchy)
list_structures = structure_match;
plot_structure_parsed = listdlg('PromptString','Select a structure to plot:', ...
'ListString',gui_data.st.safe_name(list_structures),'ListSize',[520,500], ...
'SelectionMode','single');
plot_structure = list_structures(plot_structure_parsed);
% Draw areas
draw_areas(probe_atlas_gui,slice_spacing,plot_structure);
end
function add_area_hierarchy(h,eventdata,probe_atlas_gui)
% Explore CCF hierarchy, draw selected
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Bring up hierarchical selector
plot_structure = hierarchical_select(gui_data.st);
% Draw areas
slice_spacing = 10;
draw_areas(probe_atlas_gui,slice_spacing,plot_structure);
end
function draw_areas(probe_atlas_gui,slice_spacing,plot_structure)
% Get guidata
gui_data = guidata(probe_atlas_gui);
if ~isempty(plot_structure)
% Get all areas within and below the selected hierarchy level
plot_ccf_idx = plot_structure;
% Plot the structure
atlas_downsample = 5; % (downsample atlas to make this faster)
[ap_grid_ccf,dv_grid_ccf,ml_grid_ccf] = ...
ndgrid(1:atlas_downsample:size(gui_data.av,1), ...
1:atlas_downsample:size(gui_data.av,2), ...
1:atlas_downsample:size(gui_data.av,3));
[ml_grid_bregma,ap_grid_bregma,dv_grid_bregma] = ...
transformPointsForward(gui_data.ccf_bregma_tform, ...
ml_grid_ccf,ap_grid_ccf,dv_grid_ccf);
structure_3d = isosurface(ml_grid_bregma,ap_grid_bregma,dv_grid_bregma, ...
ismember(gui_data.av(1:atlas_downsample:end, ...
1:atlas_downsample:end,1:atlas_downsample:end),plot_ccf_idx),0);
structure_alpha = 0.2;
plot_structure_color = ...
[gui_data.st.R(plot_ccf_idx),gui_data.st.G(plot_ccf_idx),gui_data.st.B(plot_ccf_idx)]/255;
gui_data.structure_plot_idx(end+1) = plot_structure;
gui_data.handles.structure_patch(end+1) = patch(gui_data.handles.axes_atlas, ...
'Vertices',structure_3d.vertices, ...
'Faces',structure_3d.faces, ...
'FaceColor',plot_structure_color,'EdgeColor','none','FaceAlpha',structure_alpha);
end
% Upload gui_data
guidata(probe_atlas_gui,gui_data);
end
function remove_area(h,eventdata,probe_atlas_gui)
% Remove previously drawn areas
% Get guidata
gui_data = guidata(probe_atlas_gui);
if ~isempty(gui_data.structure_plot_idx)
remove_structures = listdlg('PromptString','Select a structure to remove:', ...
'ListString',gui_data.st.safe_name(gui_data.structure_plot_idx));
delete(gui_data.handles.structure_patch(remove_structures))
gui_data.structure_plot_idx(remove_structures) = [];
gui_data.handles.structure_patch(remove_structures) = [];
end
% Upload gui_data
guidata(probe_atlas_gui,gui_data);
end
function visibility_slice(h,eventdata,probe_atlas_gui)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Toggle slice volume/visibility
slice_volumes = {'tv','av','none'};
new_slice_volume = slice_volumes{circshift( ...
strcmp(gui_data.handles.slice_volume,slice_volumes),[0,1])};
if strcmp(new_slice_volume,'none')
set(gui_data.handles.slice_plot,'Visible','off');
else
set(gui_data.handles.slice_plot,'Visible','on');
end
gui_data.handles.slice_volume = new_slice_volume;
guidata(probe_atlas_gui, gui_data);
update_slice(probe_atlas_gui);
% Upload gui_data
guidata(probe_atlas_gui,gui_data);
end
function visibility_brain_outline(h,eventdata,probe_atlas_gui)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Toggle brain outline visibility
current_visibility = gui_data.handles.cortex_outline.Visible;
switch current_visibility; case 'on'; new_visibility = 'off'; case 'off'; new_visibility = 'on'; end;
set(gui_data.handles.cortex_outline,'Visible',new_visibility);
% Upload gui_data
guidata(probe_atlas_gui,gui_data);
end
function visibility_grid(h,eventdata,probe_atlas_gui)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Toggle grid
current_visibility = gui_data.handles.axes_atlas.Visible;
switch current_visibility; case 'on'; new_visibility = 'off'; case 'off'; new_visibility = 'on'; end;
set(gui_data.handles.axes_atlas,'Visible',new_visibility);
% Upload gui_data
guidata(probe_atlas_gui,gui_data);
end
function visibility_probe(h,eventdata,probe_atlas_gui)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Toggle probe visibility
current_visibility = gui_data.handles.probe_ref_line.Visible;
switch current_visibility; case 'on'; new_visibility = 'off'; case 'off'; new_visibility = 'on'; end;
set(gui_data.handles.probe_ref_line,'Visible',new_visibility);
set(gui_data.handles.probe_line,'Visible',new_visibility);
% Upload gui_data
guidata(probe_atlas_gui,gui_data);
end
function visibility_3d_areas(h,eventdata,probe_atlas_gui)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Toggle plotted structure visibility
if ~isempty(gui_data.structure_plot_idx)
current_visibility = get(gui_data.handles.structure_patch(1),'Visible');
switch current_visibility; case 'on'; new_visibility = 'off'; case 'off'; new_visibility = 'on'; end;
set(gui_data.handles.structure_patch,'Visible',new_visibility);
end
% Upload gui_data
guidata(probe_atlas_gui,gui_data);
end
function visibility_darkmode(h,eventdata,probe_atlas_gui)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Toggle dark mode
curr_bg = max(get(probe_atlas_gui,'color'));