Viewing 3D images/stacks of images
Hi all, I'd used CollectionViewer from skimage.viewer before for viewing microscopy Z stacks. However, I personally felt it was a bit of a pain to use. For instance, before passing in an array of images, the image has to be stretched, otherwise, most of the time, one would end up with a "black" series of images. So, I wrote a simple function using matplotlib to view image collections, which works quite well, and I think it can be extended to display nD images with multiple sliders. def ddd(images): def _update_image(num): num = int(num) image = np.squeeze(images[num:num+1]) img_ax.set_data(image) fig.canvas.draw_idle() if images.ndim is not 3: raise ValueError("Not a 3D image.") Z, _, _ = images.shape fig, ax = plt.subplots() img_ax = ax.imshow(np.squeeze(images[0]), cmap="gray") ax.axis("off") sliderax = plt.axes([0.19, 0.05, 0.65, 0.03], facecolor="lightgoldenrodyellow") img_slider = Slider(sliderax, "Z", 0, Z-1, valfmt='%d', valinit=0) img_slider.on_changed(_update_image) plt.show() This might be a bit redundant, but I would like your thoughts on whether this might be useful for scikit-image. Some of the plugins of CollectionViewer can be rewritten for this matplotlib based approach in a much more readable fashion -- for instance, the line profile plugin. Best, -- Kesavan Subburam
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Kesavan Subburam