{ "cells": [ { "cell_type": "markdown", "id": "ac2511d6-7689-4480-b482-36dc719ec489", "metadata": {}, "source": [ "# Zoom" ] }, { "cell_type": "code", "execution_count": 1, "id": "12452471-61c6-4d32-828b-e3dc90622fe6", "metadata": {}, "outputs": [], "source": [ "import stackview\n", "from skimage.io import imread, imshow\n", "from skimage.filters import gaussian, threshold_otsu, sobel\n", "from skimage.measure import label" ] }, { "cell_type": "code", "execution_count": 2, "id": "dd7bcdad-a20b-4fe2-94c0-b588e644b2f9", "metadata": {}, "outputs": [], "source": [ "image = imread('data/Haase_MRT_tfl3d1.tif')[:,80:120,:40]" ] }, { "cell_type": "code", "execution_count": 3, "id": "edc6b6be-9381-4f84-827a-7a7844740f2a", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "
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" ], "text/plain": [ "StackViewNDArray([[[ 0, 1297, 458, ..., 992, 1221, 1755],\n", " [ 0, 839, 534, ..., 2441, 1679, 1297],\n", " [ 0, 2060, 2060, ..., 839, 610, 687],\n", " ...,\n", " [ 0, 0, 992, ..., 1221, 1526, 2289],\n", " [ 0, 0, 1297, ..., 1297, 1144, 2213],\n", " [ 0, 0, 1068, ..., 1679, 1831, 1679]],\n", "\n", " [[ 0, 916, 763, ..., 763, 1144, 1984],\n", " [ 0, 1221, 992, ..., 1679, 916, 1450],\n", " [ 0, 916, 992, ..., 1144, 992, 1679],\n", " ...,\n", " [ 0, 0, 2060, ..., 1984, 1831, 687],\n", " [ 0, 0, 1907, ..., 992, 2060, 916],\n", " [ 0, 0, 1755, ..., 1144, 2670, 1068]],\n", "\n", " [[ 0, 763, 916, ..., 1450, 839, 1221],\n", " [ 0, 1679, 992, ..., 534, 610, 763],\n", " [ 0, 305, 1602, ..., 839, 3052, 1907],\n", " ...,\n", " [ 0, 0, 305, ..., 1831, 2213, 2213],\n", " [ 0, 0, 916, ..., 763, 1068, 2289],\n", " [ 0, 0, 1221, ..., 1450, 610, 2823]],\n", "\n", " ...,\n", "\n", " [[ 0, 763, 1373, ..., 1526, 2899, 1297],\n", " [ 0, 763, 992, ..., 1297, 763, 1602],\n", " [ 0, 992, 534, ..., 1679, 534, 2289],\n", " ...,\n", " [ 0, 0, 1221, ..., 839, 534, 687],\n", " [ 0, 0, 305, ..., 916, 1907, 839],\n", " [ 0, 0, 992, ..., 1221, 1144, 1907]],\n", "\n", " [[ 0, 458, 763, ..., 2747, 1602, 763],\n", " [ 0, 458, 1068, ..., 763, 763, 1984],\n", " [ 0, 763, 1602, ..., 1297, 1450, 1221],\n", " ...,\n", " [ 0, 0, 992, ..., 534, 1907, 1144],\n", " [ 0, 0, 839, ..., 1373, 1984, 1373],\n", " [ 0, 0, 839, ..., 1526, 1221, 1373]],\n", "\n", " [[ 0, 458, 1297, ..., 992, 2365, 2136],\n", " [ 0, 381, 1068, ..., 687, 1526, 1373],\n", " [ 0, 534, 1068, ..., 1907, 1373, 305],\n", " ...,\n", " [ 0, 0, 1602, ..., 916, 458, 534],\n", " [ 0, 0, 1602, ..., 1144, 1526, 534],\n", " [ 0, 0, 839, ..., 1068, 1907, 1144]]],\n", " dtype=uint16)" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "stackview.insight(image)" ] }, { "cell_type": "markdown", "id": "0a14f513-7bfc-40e9-b472-5ba295aa5ffd", "metadata": {}, "source": [ "When working with small images, the view may be suboptimal." ] }, { "cell_type": "code", "execution_count": 4, "id": "31531f57-4f87-4eea-83cd-f38b8b1404f2", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "e45da350af1f4ed484791cf4ced277c2", "version_major": 2, "version_minor": 0 }, "text/plain": [ "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=40, width=40),)),)), IntSlider(value=60, conti…" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "stackview.slice(image)" ] }, { "cell_type": "markdown", "id": "878ea5a6-4f35-42da-bd78-2b6b4420442c", "metadata": {}, "source": [ "Thus, you can provide a `zoom_factor`." ] }, { "cell_type": "code", "execution_count": 5, "id": "b0996d45-e1a5-40f6-a085-62018fc087e1", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "1c84739b1fba4f669df55b223b44c9d4", "version_major": 2, "version_minor": 0 }, "text/plain": [ "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=400, width=400),)),)), IntSlider(value=60, con…" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "stackview.slice(image, zoom_factor=10)" ] }, { "cell_type": "markdown", "id": "16fe74de-38a4-4e58-812d-51cbe6c56c0d", "metadata": {}, "source": [ "This also works with other tools such as the `picker`." ] }, { "cell_type": "code", "execution_count": 6, "id": "21d8e810-54bf-4f9f-af10-bf07c83317b7", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "5e559af6b38e4d5387ed22627480ee9c", "version_major": 2, "version_minor": 0 }, "text/plain": [ "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=400, width=400),)),)), IntSlider(value=60, con…" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "stackview.picker(image, zoom_factor=10)" ] }, { "cell_type": "markdown", "id": "6c6de978-81d7-43de-ae30-14aa417edda6", "metadata": {}, "source": [ "If you don't like the neareast-neighbor interpolation, you can also specify a higher order of the spline-interpolation used under the hood." ] }, { "cell_type": "code", "execution_count": 7, "id": "4d8610ce-9d8f-4daf-8cc7-13f48892a0d1", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "0913f1afa93b48c28485fe1629328478", "version_major": 2, "version_minor": 0 }, "text/plain": [ "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=400, width=400),)),)), IntSlider(value=60, con…" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "stackview.picker(image, zoom_factor=10, zoom_spline_order=3)" ] }, { "cell_type": "markdown", "id": "1b31f251-ce03-4625-9058-8c1fcb781308", "metadata": {}, "source": [ "Some more zoomed views to check if `stackview` tools work." ] }, { "cell_type": "code", "execution_count": 8, "id": "971ca2de-af40-4ee5-8aa6-86bb7d7c60eb", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "5d4facc3ed2640f7bb22c2893b68a02c", "version_major": 2, "version_minor": 0 }, "text/plain": [ "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=400, width=400),)),)), IntSlider(value=60, des…" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "stackview.curtain(image, 256-image, zoom_factor=10, continuous_update=True)" ] }, { "cell_type": "code", "execution_count": 9, "id": "f4bc53f9-a4a7-4db3-9235-b3cd0b2be8c4", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "599717b5ef794828835f7aabec307152", "version_major": 2, "version_minor": 0 }, "text/plain": [ "VBox(children=(HBox(children=(VBox(children=(ImageWidget(height=512, width=508),)),)), IntSlider(value=127, co…" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "blobs = imread('data/blobs.tif')\n", "\n", "stackview.picker(label(blobs > 120), zoom_factor=2)" ] }, { "cell_type": "code", "execution_count": 10, "id": "02acd2fa-1262-45bd-bb42-562aeb443a93", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "0194d9e198ab4d4ebdb3dbe09f2344f7", "version_major": 2, "version_minor": 0 }, "text/plain": [ "HBox(children=(HBox(children=(VBox(children=(ImageWidget(height=127, width=128),)),)), HBox(children=(VBox(chi…" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "stackview.side_by_side(blobs, label(blobs > 120), zoom_factor=0.5, continuous_update=True)" ] }, { "cell_type": "code", "execution_count": 11, "id": "9c4874b1-a382-427a-8c2d-5273b802a037", "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "5e6a5b150b2b4fadb2f40400759f8cad", "version_major": 2, "version_minor": 0 }, "text/plain": [ 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