% Visualization function written for NanoLocz-lib 2025 % viewstack - Interactive viewer for 3D image stacks with customizable colormaps and labels % % USAGE: % viewstack(stack) % viewstack(stack, Info) % % DESCRIPTION: % Displays a 3D image stack slice-by-slice with an interactive GUI. % Supports mouse wheel and keyboard navigation through slices. % Allows colormap selection from predefined LUTs loaded from 'AFM_luts_full.mat'. % Provides contrast limits adjustment and optional overlay of labels from provided Info. % % INPUTS: % stack : 3D numeric array % The image stack to display. If omitted, a random 256x256x50 stack is generated. % % Info (optional) : Struct or data required by drawLabels_v2 % If provided, enables a checkbox to toggle label drawing on the images. % % FEATURES: % - Mouse wheel and arrow key navigation through slices % - Dropdown menu to select different colormaps from LUT file % - Editable contrast limits (CLim) for intensity scaling % - Checkbox to toggle overlay of labels on the current slice % % DEPENDENCIES: % - AFM_luts_full.mat : MAT file containing colormaps as structs % - drawLabels_v2 : function to overlay labels on images % % EXAMPLES: % viewstack(myStack); % viewstack(myStack, myLabelInfo); % function viewstack(stack, varargin) % varargin{1} = Info (labels) % varargin{2} = mask (same size as stack) if nargin < 1 stack = rand(256, 256, 50); end LUTs = load('AFM_luts_full.mat'); colormapNames = fieldnames(LUTs); cmapData = LUTs.(colormapNames{3}); % Default to first colormap numSlices = size(stack, 3); currentSlice = 1; hFig = figure('Name', '3D Stack Viewer Enhanced', ... 'NumberTitle', 'off', ... 'MenuBar', 'none', ... 'ToolBar', 'none', ... 'WindowScrollWheelFcn', @scrollWheelCallback, ... 'KeyPressFcn', @keyPressCallback); hAx = axes('Parent', hFig); hImg = imagesc(stack(:, :, currentSlice), 'Parent', hAx); axis image off colormap(hAx, cmapData); colorbar; title(hAx, sprintf('Slice %d of %d', currentSlice, numSlices)); % --- Draw Labels Checkbox --- if nargin > 1 hDrawLabels = uicontrol('Style', 'checkbox', ... 'String', 'Draw Labels', ... 'Units', 'normalized', ... 'Position', [0.75 0.95 0.2 0.05], ... 'Value', 0, ... 'Callback', @(src, event) updateSlice(currentSlice,varargin{:})); % Redraw current s else hDrawLabels.Value = 0; end if nargin > 2 hOverlayMask = uicontrol('Style', 'checkbox', ... 'String', 'Overlay Mask', ... 'Units', 'normalized', ... 'Position', [0.55 0.95 0.18 0.05], ... 'Value', 0, ... 'Callback', @(src, event) updateSlice(currentSlice, varargin{:})); else hOverlayMask.Value = 0; end % Dropdown for colormap selection hColormap = uicontrol('Style', 'popupmenu', ... 'String', colormapNames, ... 'Units', 'normalized', ... 'Position', [0.05 0.95 0.2 0.05], ... 'Callback', @(src, event) updateColormap()); % --- Colormap update --- function updateColormap() selectedName = colormapNames{hColormap.Value}; cmapData = LUTs.(selectedName); colormap(hAx, cmapData); end % Calculate initial contrast limits using percentiles of the first slice currentData = stack(:, :, currentSlice); sortedData = sort(currentData(:)); lowPercentile = 1; % e.g., 1st percentile highPercentile = 99; % e.g., 99th percentile climMin = sortedData(round((lowPercentile / 100) * numel(sortedData))); climMax = sortedData(round((highPercentile / 100) * numel(sortedData))); clim = [climMin, climMax]; caxis(hAx, clim); % Also update the UI edit boxes hMin.String = num2str(clim(1)); hMax.String = num2str(clim(2)); % UI controls: slider if numSlices == 1 sliderStep = [0 0]; % No movement possible enableStatus = 'off'; % Disable slider else sliderStep = [1 1] / (numSlices - 1); enableStatus = 'on'; end hSlider = uicontrol('Style', 'slider', ... 'Min', 1, 'Max', numSlices, ... 'Value', currentSlice, ... 'SliderStep', sliderStep, ... 'Enable', enableStatus, ... 'Units', 'normalized', ... 'Position', [0.2 0.02 0.6 0.05]); addlistener(hSlider, 'Value', 'PostSet', @(src, event) updateSlice(round(hSlider.Value),varargin{:})); % Intensity limits controls uicontrol('Style', 'text', 'String', 'CLim Min:', ... 'Units', 'normalized', 'Position', [0.01 0.02 0.08 0.04]); hMin = uicontrol('Style', 'edit', 'String', num2str(clim(1)), ... 'Units', 'normalized', 'Position', [0.09 0.02 0.08 0.05], ... 'Callback', @(src, event) updateCLim()); uicontrol('Style', 'text', 'String', 'CLim Max:', ... 'Units', 'normalized', 'Position', [0.81 0.02 0.08 0.04]); hMax = uicontrol('Style', 'edit', 'String', num2str(clim(2)), ... 'Units', 'normalized', 'Position', [0.89 0.02 0.08 0.05], ... 'Callback', @(src, event) updateCLim()); % --- Slice update --- % function updateSlice(idx) % currentSlice = min(max(1, idx), numSlices); % hImg.CData = stack(:, :, currentSlice); % hSlider.Value = currentSlice; % title(hAx, sprintf('Slice %d of %d', currentSlice, numSlices)); % drawnow limitrate % end function updateSlice(idx, varargin) currentSlice = min(max(1, idx), numSlices); % --- Update main image --- hImg.CData = stack(:, :, currentSlice); % --- Update slider and title --- if exist('hSlider','var') && isvalid(hSlider) hSlider.Value = currentSlice; end title(hAx, sprintf('Slice %d of %d', currentSlice, numSlices)); % --- Clear previous overlays --- delete(findall(hAx, 'Tag', 'MaskOverlay')); delete(findall(hAx, 'Type', 'line')); delete(findall(hAx, 'Type', 'text')); % --- Draw labels --- if hDrawLabels.Value && ~isempty(varargin) Info = varargin{1}; drawLabels(hAx, stack(:, :, currentSlice), currentSlice, Info, true, true); end % --- Overlay mask --- if exist('hOverlayMask','var') && hOverlayMask.Value && numel(varargin) > 1 hold on mask = varargin{2}; if size(mask,3) >= currentSlice hMask = imagesc(hAx, cat(3, zeros(size(mask(:,:,currentSlice))), ... ones(size(mask(:,:,currentSlice))), ... zeros(size(mask(:,:,currentSlice))))); hMask.AlphaData = 0.4 * double(mask(:,:,currentSlice) > 0); hMask.Tag = 'MaskOverlay'; end hold off end end % --- Contrast limits update --- function updateCLim() minVal = str2double(hMin.String); maxVal = str2double(hMax.String); if isnan(minVal) || isnan(maxVal) || minVal >= maxVal return; end caxis(hAx, [minVal, maxVal]); end % --- Mouse wheel scroll callback --- function scrollWheelCallback(~, event) delta = -event.VerticalScrollCount; updateSlice(currentSlice + delta,varargin{:}); end % --- Key press callback (arrow keys) --- function keyPressCallback(~, event) climNow = caxis(hAx); range = climNow(2) - climNow(1); switch event.Key case 'rightarrow' updateSlice(currentSlice + 1,varargin{:}); case 'leftarrow' updateSlice(currentSlice - 1,varargin{:}); case 'downarrow' if ismember('shift', event.Modifier) climNow = climNow + [-0.05 0.05] * range; else climNow = climNow + [0.05 0.05] * range; end caxis(hAx, climNow); hMin.String = num2str(climNow(1)); hMax.String = num2str(climNow(2)); case 'uparrow' if ismember('shift', event.Modifier) climNow = climNow + [0.05 -0.05] * range; else climNow = climNow - [0.05 0.05] * range; end caxis(hAx, climNow); hMin.String = num2str(climNow(1)); hMax.String = num2str(climNow(2)); end end end