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neuropixels_trajectory_explorer.m
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neuropixels_trajectory_explorer.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
% TO DO 2.0 update:
% - recording connection
function neuropixels_trajectory_explorer
%% Checks and initialize
% Check MATLAB version
matlab_version = version('-date');
if str2num(matlab_version(end-3:end)) <= 2016
error('Neuropixels Trajectory Explorer requires MATLAB 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
if ~license('test','Statistics_Toolbox')
error('MATLAB statistics toolbox required (https://uk.mathworks.com/products/statistics.html)')
end
if ~license('test','Image_Toolbox')
error('MATLAB image processing toolbox required (https://uk.mathworks.com/products/image.html)')
end
% Initialize gui_data structure
gui_data = struct;
%% Load atlas and associated data
% Load in atlas
% Find path with CCF
if ~isdeployed
% (if being run in matlab: find CCF in the matlab path)
allen_atlas_path = fileparts(which('template_volume_10um.npy'));
if isempty(allen_atlas_path)
error('CCF atlas not in MATLAB path (click ''Set path'', add folder with CCF)');
end
elseif isdeployed
% (if being run standalone: use previous user-supplied path, or query if files not available)
load('nte_paths.mat')
allen_atlas_path = nte_paths.allen_atlas_path;
if isempty(allen_atlas_path)
% (use uigetdir_workaround: matlab-issued workaround for R2018a bug)
allen_atlas_path = uigetdir_workaround([],'Select folder with Allen CCF');
end
ccf_present = false;
while ~ccf_present
tv_fn = [allen_atlas_path filesep 'template_volume_10um.npy'];
av_fn = [allen_atlas_path filesep 'annotation_volume_10um_by_index.npy'];
st_fn = [allen_atlas_path filesep 'structure_tree_safe_2017.csv'];
tv_exist = exist(tv_fn,'file');
av_exist = exist(av_fn,'file');
st_exist = exist(st_fn,'file');
ccf_files = {tv_fn,av_fn,st_fn};
ccf_exist = [tv_exist,av_exist,st_exist];
if any(~ccf_exist)
% If CCF not present in specified directory, error out
errordlg([{'Allen CCF files not found: '}, ...
ccf_files(~ccf_exist)],'Allen CCF not found, select path again');
allen_atlas_path = uigetdir_workaround([],'Allen CCF not found, select folder again:');
if allen_atlas_path == 0
return
end
else
% If all CCF files present, save path for future
nte_paths.allen_atlas_path = allen_atlas_path;
nte_paths_fn = which('nte_paths.mat');
save(nte_paths_fn,'nte_paths');
ccf_present = true;
end
end
end
% Load CCF components
tv = readNPY([allen_atlas_path filesep 'template_volume_10um.npy']); % grey-scale "background signal intensity"
av = readNPY([allen_atlas_path filesep 'annotation_volume_10um_by_index.npy']); % the number at each pixel labels the area, see note below
st = load_structure_tree([allen_atlas_path filesep 'structure_tree_safe_2017.csv']); % a table of what all the labels mean
% Create CCF colormap
% (copied from cortex-lab/allenCCF/setup_utils
ccf_color_hex = st.color_hex_triplet;
ccf_color_hex(cellfun(@numel,ccf_color_hex)==5) = {'019399'}; % special case where leading zero was evidently dropped
ccf_cmap_c1 = cellfun(@(x)hex2dec(x(1:2)), ccf_color_hex, 'uni', false);
ccf_cmap_c2 = cellfun(@(x)hex2dec(x(3:4)), ccf_color_hex, 'uni', false);
ccf_cmap_c3 = cellfun(@(x)hex2dec(x(5:6)), ccf_color_hex, 'uni', false);
ccf_cmap = horzcat(vertcat(ccf_cmap_c1{:}),vertcat(ccf_cmap_c2{:}),vertcat(ccf_cmap_c3{:}))./255;
%% Make transform matrix from CCF to bregma/mm coordinates
% Set average stereotaxic bregma-lambda distance, set initial scale to 1
bregma_lambda_distance_avg = 4.1; % Currently approximation
% (translation values from our bregma estimate: AP/ML from Paxinos, DV from
% rough MRI estimate)
bregma_ccf = [570.5,520,44]; % [ML,AP,DV]
ccf_translation_tform = eye(4)+[zeros(3,4);-bregma_ccf,0];
% (scaling "Toronto MRI transform", reflect AP/ML, convert 10um to 1mm)
scale = [0.952,-1.031,0.885]./100; % [ML,AP,DV]
ccf_scale_tform = eye(4).*[scale,1]';
% (rotation values from IBL estimate)
ap_rotation = 5; % tilt the CCF 5 degrees nose-up
ccf_rotation_tform = ...
[1 0 0 0; ...
0 cosd(ap_rotation) -sind(ap_rotation) 0; ...
0 sind(ap_rotation) cosd(ap_rotation) 0; ...
0 0 0 1];
% Create transform matrix (operates as [ML,AP,DV])
ccf_bregma_tform_matrix = ccf_translation_tform*ccf_scale_tform*ccf_rotation_tform;
ccf_bregma_tform = affine3d(ccf_bregma_tform_matrix);
%% Make GUI axes and objects
% Set up the gui
screen_size_px = get(0,'screensize');
gui_aspect_ratio = 1.7; % width/length
gui_width_fraction = 0.6; % fraction of screen width to occupy
gui_width_px = screen_size_px(3).*gui_width_fraction;
gui_position = [...
(screen_size_px(3)-gui_width_px)/2, ... % left x
(screen_size_px(4)-gui_width_px/gui_aspect_ratio)/2, ... % bottom y
gui_width_px,gui_width_px/gui_aspect_ratio]; % width, height
probe_atlas_gui = figure('Toolbar','none','Menubar','none','color','w', ...
'Name','Neuropixels Trajectory Explorer', ...
'Units','pixels','Position',gui_position, ...
'CloseRequestFcn',{@gui_close});
% Set up the atlas axes
axes_atlas = axes('Position',[-0.08,0.05,1,0.9],'ZDir','reverse');
axis(axes_atlas,'vis3d','equal','off','manual'); hold(axes_atlas,'on');
view([30,150]);
caxis([0 300]);
xlim([-5,5]);ylim([-8,6]);zlim([-1,6.5]);
grid_spacing = 0.5;
set(gca,'XTick',floor(min(xlim)):grid_spacing:ceil(max(xlim)));
set(gca,'YTick',floor(min(ylim)):grid_spacing:ceil(max(ylim)));
set(gca,'ZTick',floor(min(zlim)):grid_spacing:ceil(max(zlim)));
grid on;
% Set up the text to display coordinates
gui_position_px = getpixelposition(probe_atlas_gui);
probe_coordinates_text = annotation('textbox','String','No probe selected', ...
'Units','normalized','Position',[0,0,1,1],'VerticalAlignment','top', ...
'FontSize',12,'FontName','Consolas','PickableParts','none');
% Set up the probe area axes
axes_probe_areas = axes('Position',[0.80,0.01,0.15,0.95],'TickDir','in');
axes_probe_areas.ActivePositionProperty = 'position';
probe_areas_plot = image(axes_probe_areas,[0,1],0,0);
axes_probe_areas_probelimits = ...
rectangle(axes_probe_areas, ...
'position',[min(xlim(axes_probe_areas)),0,0,0], ...
'edgecolor','b','linewidth',5);
set(axes_probe_areas,'FontSize',12);
set(axes_probe_areas,'XTick','','YColor','k','YDir','reverse');
ylabel(axes_probe_areas,'Depth (mm)');
axes_probe_areas.YAxisLocation = 'right';
title(axes_probe_areas,'Probe areas');
%% Create menu/buttons
probe_controls_menu = uimenu(probe_atlas_gui,'Text','Probe controls');
uimenu(probe_controls_menu,'Text','Display controls','MenuSelectedFcn',{@popup_controls,probe_atlas_gui});
uimenu(probe_controls_menu,'Text','Add probe','MenuSelectedFcn',{@probe_add,probe_atlas_gui});
uimenu(probe_controls_menu,'Text','Remove selected probe','MenuSelectedFcn',{@probe_remove,probe_atlas_gui});
uimenu(probe_controls_menu,'Text','Set entry','MenuSelectedFcn',{@set_probe_entry,probe_atlas_gui});
uimenu(probe_controls_menu,'Text','Set endpoint','MenuSelectedFcn',{@set_probe_endpoint,probe_atlas_gui});
scaling_menu = uimenu(probe_atlas_gui,'Text','Brain scaling');
uimenu(scaling_menu,'Text','Set bregma-lambda distance','MenuSelectedFcn',{@set_bregma_lambda_distance,probe_atlas_gui});
mesh_areas_menu = uimenu(probe_atlas_gui,'Text','3D areas');
uimenu(mesh_areas_menu,'Text','List areas','MenuSelectedFcn',{@add_area_list,probe_atlas_gui});
uimenu(mesh_areas_menu,'Text','Search areas','MenuSelectedFcn',{@add_area_search,probe_atlas_gui});
uimenu(mesh_areas_menu,'Text','Hierarchy areas','MenuSelectedFcn',{@add_area_hierarchy,probe_atlas_gui});
uimenu(mesh_areas_menu,'Text','Remove areas','MenuSelectedFcn',{@remove_area,probe_atlas_gui});
display_menu = uimenu(probe_atlas_gui,'Text','Display');
name_menu = uimenu(display_menu,'Text','Trajectory areas');
uimenu(name_menu,'Text','Probe position','MenuSelectedFcn',{@set_areas_probe,probe_atlas_gui},'Checked','on')
uimenu(name_menu,'Text','Full trajectory','MenuSelectedFcn',{@set_areas_trajectory,probe_atlas_gui},'Checked','off')
name_menu = uimenu(display_menu,'Text','Region names');
uimenu(name_menu,'Text','Acronym','MenuSelectedFcn',{@set_name_acronym,probe_atlas_gui},'Checked','on')
uimenu(name_menu,'Text','Full','MenuSelectedFcn',{@set_name_full,probe_atlas_gui})
slice_menu = uimenu(display_menu,'Text','Slice');
uimenu(slice_menu,'Text','Anatomical','MenuSelectedFcn',{@visibility_tv_slice,probe_atlas_gui},'Checked','off')
uimenu(slice_menu,'Text','Annotated','MenuSelectedFcn',{@visibility_av_slice,probe_atlas_gui})
object_menu = uimenu(display_menu,'Text','Objects');
uimenu(object_menu,'Text','Brain outline','MenuSelectedFcn',{@visibility_brain_outline,probe_atlas_gui},'Checked','on');
uimenu(object_menu,'Text','Grid','MenuSelectedFcn',{@visibility_grid,probe_atlas_gui});
uimenu(object_menu,'Text','Probe','MenuSelectedFcn',{@visibility_probe,probe_atlas_gui},'Checked','on');
uimenu(object_menu,'Text','3D areas','MenuSelectedFcn',{@visibility_3d_areas,probe_atlas_gui},'Checked','on');
uimenu(object_menu,'Text','Dark mode','MenuSelectedFcn',{@visibility_darkmode,probe_atlas_gui});
connect_menu = uimenu(probe_atlas_gui,'Text','Connect');
manipulator_menu = uimenu(connect_menu,'Text','Manipulator');
uimenu(manipulator_menu,'Text','New Scale MPM','MenuSelectedFcn',{@connect_newscale,probe_atlas_gui});
uimenu(manipulator_menu,'Text','Scientifica Patchstar','MenuSelectedFcn',{@connect_scientifica,probe_atlas_gui});
record_menu = uimenu(connect_menu,'Text','Recording');
uimenu(record_menu,'Text','OpenEphys','MenuSelectedFcn',{@connect_openephys,probe_atlas_gui});
uimenu(record_menu,'Text','SpikeGLX','MenuSelectedFcn',{@connect_spikeglx,probe_atlas_gui});
uimenu(record_menu,'Text','Set recording slot','MenuSelectedFcn',{@set_probe_recording_slot,probe_atlas_gui});
saveload_menu = uimenu(probe_atlas_gui,'Text','Save/Load');
uimenu(saveload_menu,'Text','Save positions','MenuSelectedFcn',{@save_probe_positions,probe_atlas_gui});
uimenu(saveload_menu,'Text','Load positions','MenuSelectedFcn',{@load_probe_positions,probe_atlas_gui});
%%% Buttons
button_fontsize = 12;
% View angle buttons
button_position = [0,0,0.1,0.05];
view_button_h(1) = uicontrol('Parent',probe_atlas_gui,'Style','pushbutton','FontSize',button_fontsize, ...
'Units','normalized','Position',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',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',button_position,'String','Horizontal','Callback',{@view_horizontal,probe_atlas_gui});
align(view_button_h,'fixed',0.1,'middle');
%% Store initial GUI data
gui_data.tv = tv; % Intensity atlas
gui_data.av = av; % Annotated atlas
gui_data.st = st; % Labels table
gui_data.bregma_lambda_distance_avg = bregma_lambda_distance_avg; % Average bregma-lambda distance
gui_data.bregma_lambda_distance_curr = bregma_lambda_distance_avg; % Set current as average
gui_data.cmap = ccf_cmap; % Atlas colormap
gui_data.ccf_bregma_tform_ref = ccf_bregma_tform; % Reference CCF-bregma transform
gui_data.ccf_bregma_tform = ccf_bregma_tform; % CCF-bregma transform to use
gui_data.structure_plot_idx = []; % Plotted structures
% Store handles
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.axes_probe_areas_probelimits = axes_probe_areas_probelimits; % Probe location on area plot
gui_data.handles.probe_areas_plot = probe_areas_plot; % Color-coded probe regions
gui_data.handles.slice_plot = surface(axes_atlas,'EdgeColor','none','Visible','off'); % Slice on 3D atlas
gui_data.handles.slice_volume = 'tv'; % The volume shown in the slice
gui_data.probe_coordinates_text = probe_coordinates_text; % Probe coordinates text
% Make 3D rotation the default state
h = rotate3d(axes_atlas);
h.Enable = 'on';
h.ButtonDownFilter = @rotate_clickable; % enable click-to-select during rotation
% 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);
% Draw brain outline
draw_brain(probe_atlas_gui);
end
function gui_close(probe_atlas_gui,eventdata)
% When closing gui, make sure all timers are ended
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Find all timers derived by the gui
if ~isdeployed
% (only necessary if running from matlab)
curr_timers = timerfindall;
if ~isempty(curr_timers)
gui_timers_idx = cellfun(@(x) x{2} == probe_atlas_gui,{curr_timers(:).TimerFcn});
stop(curr_timers(gui_timers_idx));
delete(curr_timers(gui_timers_idx));
end
end
% Close the gui
delete(probe_atlas_gui);
end
%% Probe controls and slice/brain updating
function key_press(probe_atlas_gui,eventdata)
% Get guidata
gui_data = guidata(probe_atlas_gui);
% If no probes are selected, do nothing
if ~isfield(gui_data,'selected_probe') || isempty(gui_data.selected_probe)
return
end
% Step sizes
step_size_position = 0.1; % position, mm
step_size_rotation = 10; % angle, deg
% Update probe coordinates
ap_offset = 0;
ml_offset = 0;
angle_ap_offset = 0;
angle_ml_offset = 0;
update_probe_flag = false;
switch eventdata.Key
case 'uparrow'
if isempty(eventdata.Modifier)
ap_offset = step_size_position;
elseif any(strcmp(eventdata.Modifier,'shift'))
angle_ap_offset = step_size_position;
elseif any(strcmp(eventdata.Modifier,'alt'))
gui_data.probe(gui_data.selected_probe).dv = ...
gui_data.probe(gui_data.selected_probe).dv - step_size_position;
update_probe_flag = true;
guidata(probe_atlas_gui,gui_data);
end
case 'downarrow'
if isempty(eventdata.Modifier)
ap_offset = -step_size_position;
elseif any(strcmp(eventdata.Modifier,'shift'))
angle_ap_offset = -step_size_position;
elseif any(strcmp(eventdata.Modifier,'alt'))
gui_data.probe(gui_data.selected_probe).dv = ...
gui_data.probe(gui_data.selected_probe).dv + step_size_position;
update_probe_flag = true;
guidata(probe_atlas_gui,gui_data);
end
case 'leftarrow'
if isempty(eventdata.Modifier)
ml_offset = -step_size_position;
elseif any(strcmp(eventdata.Modifier,'shift'))
angle_ml_offset = -step_size_position;
elseif any(strcmp(eventdata.Modifier,'control'))
gui_data.probe(gui_data.selected_probe).angle = ...
mod(gui_data.probe(gui_data.selected_probe).angle + ...
[0;0;-step_size_rotation],360);
update_probe_flag = true;
end
case 'rightarrow'
if isempty(eventdata.Modifier)
ml_offset = step_size_position;
elseif any(strcmp(eventdata.Modifier,'shift'))
angle_ml_offset = step_size_position;
elseif any(strcmp(eventdata.Modifier,'control'))
gui_data.probe(gui_data.selected_probe).angle = ...
mod(gui_data.probe(gui_data.selected_probe).angle + ...
[0;0;+step_size_rotation],360);
update_probe_flag = true;
end
end
% Draw updated trajectory
old_trajectory_vector = get(gui_data.probe(gui_data.selected_probe).trajectory,{'XData','YData'});
set(gui_data.probe(gui_data.selected_probe).trajectory,'XData', ...
old_trajectory_vector{1} + repmat(ml_offset,1,2) + [0,angle_ml_offset]);
set(gui_data.probe(gui_data.selected_probe).trajectory,'YData', ...
old_trajectory_vector{2} + repmat(ap_offset,1,2) + [0,angle_ap_offset]);
% Update position (only if insertion point doesn't change)
if update_probe_flag
update_probe_position(probe_atlas_gui);
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);
% If no probes are selected, do nothing
if ~isfield(gui_data,'selected_probe') || isempty(gui_data.selected_probe)
return
end
% On any key release: update the probe coordinates/position and slice
update_probe_position(probe_atlas_gui);
update_probe_areas_coordinates(probe_atlas_gui);
update_slice(probe_atlas_gui);
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 trajectory and probe location
trajectory_position = cell2mat(get( ...
gui_data.probe(gui_data.selected_probe).trajectory, ...
{'XData','YData','ZData'})')';
probe_position = permute(cell2mat(permute(get( ...
gui_data.probe(gui_data.selected_probe).line, ...
{'XData','YData','ZData'}),[1,3,2])),[2,3,1]);
if size(probe_position,3) > 1
% If multiple shanks: use vector across shank points
plot_vector = diff(permute(probe_position(1,:,[1,end]),[3,2,1]));
else
% Otherwise: use plane perpendicular to camera viewpoint
% Get current position of camera
curr_campos = campos(gui_data.handles.axes_atlas);
% Get trajectory-camera vector
trajectory_camera_vector = trajectory_position(1,:) - curr_campos;
% Get the vector to plot the plane in (along with probe vector)
plot_vector = cross(trajectory_camera_vector,diff(trajectory_position,[],1));
end
% Get the normal vector of the plane
normal_vector = cross(plot_vector,diff(trajectory_position));
% Get the plane offset through the probe
plane_offset = -(normal_vector*trajectory_position(1,:)');
% 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 = 0.03; % 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
plane_coords = ...
round([plane_ap_ccf(:),plane_dv_ccf(:),plane_ml_ccf(:)]);
plane_coords_inbounds = all(plane_coords > 0 & ...
plane_coords <= size(gui_data.tv),2);
plane_idx = sub2ind(size(gui_data.tv), ...
plane_coords(plane_coords_inbounds,1), ...
plane_coords(plane_coords_inbounds,2), ...
plane_coords(plane_coords_inbounds,3));
switch gui_data.handles.slice_volume
case 'tv'
curr_slice = nan(size(plane_ap_ccf));
curr_slice(plane_coords_inbounds) = gui_data.tv(plane_idx);
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 = nan(size(plane_ap_ccf));
curr_slice(plane_coords_inbounds) = gui_data.av(plane_idx);
curr_slice(curr_slice <= 1) = NaN; % threshold values
curr_slice(boundarymask(max(curr_slice,0),4)) = 0;
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);
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)', ...
'Rotation angle'};
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 = new_probe_position(3:5);
% 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)]);
[x,y,z] = sph2cart( ...
deg2rad(90-probe_angle(1)), ...
deg2rad(180+probe_angle(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];
trajectory_vector = [probe_ref_top;probe_ref_bottom]';
set(gui_data.probe(gui_data.selected_probe).trajectory, ...
'XData',trajectory_vector(1,:), ...
'YData',trajectory_vector(2,:), ...
'ZData',trajectory_vector(3,:));
% Upload gui_data
gui_data.probe(gui_data.selected_probe).angle = probe_angle;
guidata(probe_atlas_gui, gui_data);
% Update probe and slice
update_probe_position(probe_atlas_gui);
update_probe_areas_coordinates(probe_atlas_gui);
update_slice(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)', ...
'Rotation angle'};
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);
probe_angle = new_probe_position(4:6);
% Convert degrees to radians
probe_angle_rad = deg2rad(probe_angle(1:2));
% 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);
% 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];
trajectory_vector = [probe_ref_top;probe_ref_bottom]';
set(gui_data.probe(gui_data.selected_probe).trajectory, ...
'XData',trajectory_vector(1,:), ...
'YData',trajectory_vector(2,:), ...
'ZData',trajectory_vector(3,:));
% Upload gui_data
gui_data.probe(gui_data.selected_probe).angle = probe_angle;
guidata(probe_atlas_gui, gui_data);
% Update probe and slice
update_probe_position(probe_atlas_gui);
update_probe_areas_coordinates(probe_atlas_gui);
update_slice(probe_atlas_gui);
end
function gui_data = update_probe_position(probe_atlas_gui)
% Update the probe position position relative to trajectory vector angles,
% stored rotation angle, and stored DV position
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Get the trajectory angle
trajectory_vector = cell2mat( ...
get(gui_data.probe(gui_data.selected_probe).trajectory, ...
{'XData','YData','ZData'})');
[trajectory_azimuth_sph,trajectory_elevation_sph] = cart2sph( ...
diff(trajectory_vector(1,:)), ...
diff(trajectory_vector(2,:)), ...
diff(trajectory_vector(3,:)));
% Get probe shank coordinates relative to rotation
probe_rotation_rad = -deg2rad(gui_data.probe(gui_data.selected_probe).angle(3));
probe_angle_rad = [probe_rotation_rad, ...
pi/2-trajectory_elevation_sph, ...
trajectory_azimuth_sph+pi/2];
% Create rotation transform matricies
R_shank = [cos(probe_angle_rad(1)) -sin(probe_angle_rad(1)) 0; sin(probe_angle_rad(1)) cos(probe_angle_rad(1)) 0; 0 0 1];
R_elevation = [1 0 0; 0 cos(probe_angle_rad(2)) -sin(probe_angle_rad(2)); 0 sin(probe_angle_rad(2)) cos(probe_angle_rad(2))];
R_azimuth = [cos(probe_angle_rad(3)) -sin(probe_angle_rad(3)) 0; sin(probe_angle_rad(3)) cos(probe_angle_rad(3)) 0; 0 0 1];
R_probe = R_azimuth*R_elevation*R_shank;
% Rotate and translate default shanks to follow trajectory
shank_translate = trajectory_vector(:,1); % (move to trajectory top)
shank_ref_vec = gui_data.probe(gui_data.selected_probe).reference_vector;
shank_ref_vec_flat = reshape(permute(shank_ref_vec,[3,1,2]),3,[]);
shank_vector_flat = R_probe*shank_ref_vec_flat + shank_translate;
shank_vector = permute(reshape(shank_vector_flat,3,2,[]),[2 3 1]);
% Get current probe (reference shank) DV position
ref_shank = gui_data.probe(gui_data.selected_probe).ref_shank;
dv_target = gui_data.probe(gui_data.selected_probe).dv;
dv_ref = shank_vector(:,ref_shank,3);
new_probe_position = reshape(interp1(dv_ref, ...
reshape(shank_vector,2,[]), ...
dv_target-[diff(dv_ref),0],'linear','extrap'),size(shank_vector));
% Update shank line positions
for curr_shank = 1:size(shank_vector,2)
gui_data.probe(gui_data.selected_probe).line(curr_shank).XData = new_probe_position(:,curr_shank,1);
gui_data.probe(gui_data.selected_probe).line(curr_shank).YData = new_probe_position(:,curr_shank,2);
gui_data.probe(gui_data.selected_probe).line(curr_shank).ZData = new_probe_position(:,curr_shank,3);
end
% Update probe angles
gui_data.probe(gui_data.selected_probe).angle(1:2) = ...
mod(rad2deg([-trajectory_azimuth_sph,trajectory_elevation_sph]) + ...
[90,0],360);
% Upload gui_data
guidata(probe_atlas_gui, gui_data);
end
function update_probe_areas_coordinates(probe_atlas_gui,varargin)
% Update the areas and coordinates for the current probe position
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Get current probe location
probe_vector = permute(cell2mat(permute(get( ...
gui_data.probe(gui_data.selected_probe).line, ...
{'XData','YData','ZData'}),[1,3,2])),[2,3,1]);
n_shanks = size(probe_vector,3);
% Interpolate to extremes of probe range
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)]);
sample_points = (-max_ref_length:0.001:max_ref_length)';
probe_sample_points_bregma = reshape( ...
interp1([0,gui_data.probe(gui_data.selected_probe).length], ...
reshape(probe_vector,2,[]), ...
sample_points,'linear','extrap'), ...
[length(sample_points),size(probe_vector,[2,3])]);
probe_sample_points_ccf_flat = ...
round(transformPointsInverse(gui_data.ccf_bregma_tform, ...
reshape(permute(probe_sample_points_bregma,[1,3,2]),[],3)));
inbounds_idx = all(probe_sample_points_ccf_flat > 0 & ...
probe_sample_points_ccf_flat <= size(gui_data.av,[3,1,2]),2);
probe_sample_ccf_idx = ...
sub2ind(size(gui_data.av), ...
probe_sample_points_ccf_flat(inbounds_idx,2), ...
probe_sample_points_ccf_flat(inbounds_idx,3), ...
probe_sample_points_ccf_flat(inbounds_idx,1));
probe_areas = ones(length(sample_points),n_shanks);
probe_areas(inbounds_idx) = gui_data.av(probe_sample_ccf_idx);
% Only plot areas that have index >1 (in-brain)
plot_probe_areas_idx = find(any(probe_areas > 1,2));
probe_areas_plot = probe_areas(plot_probe_areas_idx,:);
% Get insertion coordinate
ref_shank = gui_data.probe(gui_data.selected_probe).ref_shank;
insertion_point = probe_sample_points_bregma( ...
plot_probe_areas_idx(find(probe_areas_plot(:,ref_shank) > 1,1,'first')),:,ref_shank);
if isempty(insertion_point)
% (don't update if there isn't an insertion point)
set(gui_data.probe_coordinates_text,'String','Probe trajectory is outside brain');
return
end
% Get current depth of probe relative to insertion coordinate
probe_depth = pdist2(insertion_point,probe_vector(2,:,ref_shank));
% Get area depths relative to insertion coordinate
probe_areas_plot_depth = pdist2(insertion_point, ...
probe_sample_points_bregma(plot_probe_areas_idx,:,ref_shank))';
% Get colors for all areas (draw white lines between areas)
probe_areas_hexcolors = gui_data.st.color_hex_triplet(probe_areas_plot);
probe_areas_rgbcolors = cell2mat(cellfun(@(x) ...
permute(hex2dec({x(1:2),x(3:4),x(5:6)})'./255,[1,3,2]), ...
probe_areas_hexcolors,'uni',false));
for curr_shank = 1:n_shanks
probe_areas_rgbcolors(imdilate(boundarymask( ...
probe_areas_plot(:,curr_shank)),ones(20,1)),curr_shank,:) = 1;
end
% Get boundaries, centers, and labels for all areas
if ~isfield(gui_data,'display_region_name')
gui_data.display_region_name = 'acronym';
end
probe_area_boundaries = cell(n_shanks,1);
probe_area_centers = cell(n_shanks,1);
probe_area_labels = cell(n_shanks,1);
probe_area_hexcolors = cell(n_shanks,1);
for curr_shank = 1:n_shanks
shank_areas_plot = probe_areas_plot(:,curr_shank);
shank_areas_boundaries_idx = intersect(unique( ...
[find(shank_areas_plot ~= 1,1,'first'); ...
find(diff(shank_areas_plot) ~= 0); ...
find(shank_areas_plot ~= 1,1,'last')]), ...
find(shank_areas_plot ~= 1));
shank_areas_centers_idx = round(shank_areas_boundaries_idx(1:end-1) + ...
diff(shank_areas_boundaries_idx)/2);
probe_area_boundaries{curr_shank} = ...
probe_areas_plot_depth(shank_areas_boundaries_idx);
probe_area_centers{curr_shank} = ...
probe_areas_plot_depth(shank_areas_centers_idx);
probe_area_labels{curr_shank} = ...
gui_data.st.(gui_data.display_region_name)(probe_areas_plot(shank_areas_centers_idx,curr_shank));
probe_area_hexcolors{curr_shank} = ...
probe_areas_hexcolors(shank_areas_centers_idx);
end
% Update area plot and labels
set(gui_data.handles.axes_probe_areas, ...
'YTick',floor(probe_areas_plot_depth(1)):0.5: ...
ceil(probe_areas_plot_depth(end)));
set(gui_data.handles.probe_areas_plot, ...
'XData',1:n_shanks, ...
'YData',probe_areas_plot_depth, ...
'CData',probe_areas_rgbcolors);
probe_area_shank = cellfun(@(x,shank) ones(length(x),1).*shank, ...
probe_area_centers,num2cell(1:n_shanks)','uni',false);
delete(findobj(gui_data.handles.axes_probe_areas,'Type','text'));
text_h = text(gui_data.handles.axes_probe_areas, ...
vertcat(probe_area_shank{:}), ...
vertcat(probe_area_centers{:}),vertcat(probe_area_labels{:}), ...
'FontSize',12,'HorizontalAlignment','center','clipping','on');
switch gui_data.display_region_name
case 'acronym'
set(text_h,'clipping','on')
case 'safe_name'
set(text_h,'clipping','off')
end
% Update probe insertion point
[gui_data.probe(gui_data.selected_probe).insertion_point.XData, ...
gui_data.probe(gui_data.selected_probe).insertion_point.YData, ...
gui_data.probe(gui_data.selected_probe).insertion_point.ZData] = ...
deal(insertion_point(1),insertion_point(2),insertion_point(3));
% Update area plot (user-selected zoom as probe or full trajectory)
probe_depth_limits = probe_depth - ...
[gui_data.probe(gui_data.selected_probe).length,0];
gui_data.handles.axes_probe_areas_probelimits.Position = ...
[0.5,probe_depth_limits(1),n_shanks,diff(probe_depth_limits)];
if ~isfield(gui_data,'display_areas')
gui_data.display_areas = 'probe';
end
axis(gui_data.handles.axes_probe_areas,'tight');
switch gui_data.display_areas
case 'probe'
% Set limits to probe, turn off probe box
ylim(gui_data.handles.axes_probe_areas,probe_depth_limits)
gui_data.handles.axes_probe_areas_probelimits.Visible = 'off';
title(gui_data.handles.axes_probe_areas,'Probe areas');
case 'trajectory'
% Set limits to whole trajectory, turn off probe box
ylim(gui_data.handles.axes_probe_areas,prctile(probe_areas_plot_depth,[0,100]));
gui_data.handles.axes_probe_areas_probelimits.Visible = 'on';
title(gui_data.handles.axes_probe_areas,'Trajectory areas');
end
% Update the text
% (manipulator angles)
probe_angle_text = sprintf('Angle: %.0f%c azimuth, %.0f%cH/%.0f%cV elevation, %.0f%c rotation', ...
gui_data.probe(gui_data.selected_probe).angle(1),char(176), ...
gui_data.probe(gui_data.selected_probe).angle(2),char(176), ...
90-gui_data.probe(gui_data.selected_probe).angle(2),char(176), ...
gui_data.probe(gui_data.selected_probe).angle(3),char(176));
% (probe insertion point and depth)
probe_insertion_text = sprintf('Insertion: % .2f AP, % .2f ML, % .2f DV', ...
insertion_point(2),insertion_point(1),insertion_point(3));
% (probe tip)
probe_tip_text = sprintf('Tip: % .2f AP, % .2f ML, % .2f DV, % .2f depth (Z)', ...
probe_vector(2,[2,1,3],ref_shank),probe_depth);
% (bregma-lambda distance for scaling)
bregma_lambda_text = sprintf('Bregma-Lambda distance: % .2f mm', ...
gui_data.bregma_lambda_distance_curr);
% (connection status)
manipulator_text = [];
recording_text = [];
if isfield(gui_data,'connection')
if isfield(gui_data.connection,'manipulator')
manipulator_text = sprintf('Connected manipulator: %s', ...
gui_data.connection.manipulator.model);
end
if isfield(gui_data.connection,'recording')
recording_text = sprintf('Connected recording: %s', ...
gui_data.connection.recording.software);
end
end
% (combine and update)
probe_text = {probe_angle_text,probe_insertion_text, ...
probe_tip_text,bregma_lambda_text, ...
manipulator_text,recording_text};
set(gui_data.probe_coordinates_text,'String',probe_text(cellfun(@(x) ~isempty(x),probe_text)));
% If recording software is connected, send areas for display
if isfield(gui_data,'connection') && ...
isfield(gui_data.connection,'recording')
send_recording_areas(gui_data, ...
probe_depth, ...
probe_area_boundaries, ...
probe_area_labels, ...
probe_area_hexcolors);
end
% Upload gui_data
guidata(probe_atlas_gui, gui_data);
end
function update_brain_scale(probe_atlas_gui,bregma_lambda_distance)
% Update the scaling of the brain based on the bregma-lambda distance
% Get guidata
gui_data = guidata(probe_atlas_gui);
% Add "rescaling" message
set(gui_data.probe_coordinates_text,'String','RESCALING BRAIN...');
set(gui_data.probe_coordinates_text,'Color','r');
drawnow;
% Get the sizing scale of this mouse to the reference atlas
mouse_scale = bregma_lambda_distance/ ...
gui_data.bregma_lambda_distance_avg;
% Apply scale to reference transform and set to new transform
mouse_scale_tform = eye(4).*[repmat(mouse_scale,3,1);1];
gui_data.ccf_bregma_tform.T = gui_data.ccf_bregma_tform_ref.T*mouse_scale_tform;
% Update current bregma-lambda distance
gui_data.bregma_lambda_distance_curr = bregma_lambda_distance;
% Upload gui_data
guidata(probe_atlas_gui, gui_data);
% Redraw to new scale:
% - Brain outline
draw_brain(probe_atlas_gui);
% - 3D areas
for redraw_area = gui_data.structure_plot_idx
draw_areas(probe_atlas_gui,redraw_area)
end
% - Slice
update_slice(probe_atlas_gui);
% Update probe coordinates
update_probe_areas_coordinates(probe_atlas_gui);
% Restore text color
set(gui_data.probe_coordinates_text,'Color','k')
end
%% Control 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);
% (hacky - switch focus back to axes)
set(h,'enable','off');drawnow;set(h,'enable','on');
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);
% (hacky - switch focus back to axes)
set(h,'enable','off');drawnow;set(h,'enable','on');
end