{ "cells": [ { "cell_type": "markdown", "id": "dca63629", "metadata": { "id": "dca63629" }, "source": [ "# stackview on google colab\n", "Interactive image stack viewing in jupyter notebooks based on\n", "[ipycanvas](https://ipycanvas.readthedocs.io/) and\n", "[ipywidgets](https://ipywidgets.readthedocs.io/en/latest/).\n", "\n", "In this notebook we demonstate its usage on google colab.\n", "\n", "[Run this notebook in google colab](https://colab.research.google.com/github/haesleinhuepf/stackview/blob/master/docs/colab_demo.ipynb)\n", "\n", "## Installation\n", "After starting a new session on google colab, you need to install stackview first.\n", "\n", "Also note: The make stackview work in google colab, you need to install ipycanvas==0.11 ([read why](https://github.com/martinRenou/ipycanvas/issues/170#issuecomment-1119200238))." ] }, { "cell_type": "code", "execution_count": 1, "id": "fbe9e100-c5cc-4d59-b105-cd5ec72e041d", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "fbe9e100-c5cc-4d59-b105-cd5ec72e041d", "outputId": "bb3853e6-8a49-4bac-d575-15d6f24711d7" }, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "Requirement already satisfied: stackview==0.16.0 in /usr/local/lib/python3.11/dist-packages (0.16.0)\n", "Requirement already satisfied: ipycanvas==0.11 in /usr/local/lib/python3.11/dist-packages (0.11.0)\n", "Requirement already satisfied: numpy!=1.19.4 in /usr/local/lib/python3.11/dist-packages (from stackview==0.16.0) (2.0.2)\n", "Requirement already satisfied: ipywidgets in /usr/local/lib/python3.11/dist-packages (from stackview==0.16.0) (7.7.1)\n", "Requirement already satisfied: scikit-image in /usr/local/lib/python3.11/dist-packages (from stackview==0.16.0) (0.25.2)\n", "Requirement already satisfied: ipyevents in /usr/local/lib/python3.11/dist-packages (from stackview==0.16.0) (2.0.2)\n", "Requirement already satisfied: toolz in /usr/local/lib/python3.11/dist-packages (from 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(2.22)\n", "Requirement already satisfied: anyio>=3.1.0 in /usr/local/lib/python3.11/dist-packages (from jupyter-server<3,>=1.8->notebook-shim>=0.2.3->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->stackview==0.16.0) (4.9.0)\n", "Requirement already satisfied: websocket-client in /usr/local/lib/python3.11/dist-packages (from jupyter-server<3,>=1.8->notebook-shim>=0.2.3->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->stackview==0.16.0) (1.8.0)\n", "Requirement already satisfied: idna>=2.8 in /usr/local/lib/python3.11/dist-packages (from anyio>=3.1.0->jupyter-server<3,>=1.8->notebook-shim>=0.2.3->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->stackview==0.16.0) (3.10)\n", "Requirement already satisfied: sniffio>=1.1 in /usr/local/lib/python3.11/dist-packages (from anyio>=3.1.0->jupyter-server<3,>=1.8->notebook-shim>=0.2.3->nbclassic>=0.4.7->notebook>=4.4.1->widgetsnbextension~=3.6.0->ipywidgets->stackview==0.16.0) (1.3.1)\n" ] } ], "source": [ "!pip install stackview==0.16.0 ipycanvas==0.11" ] }, { "cell_type": "markdown", "id": "79a8abbc", "metadata": { "id": "79a8abbc" }, "source": [ "If you ran this for the first time, you need to restart your session.\n", "\n", "## Usage\n", "First we test the installation by importing the libraries we're going to use" ] }, { "cell_type": "code", "execution_count": 2, "id": "ca154076", "metadata": { "id": "ca154076", "tags": [] }, "outputs": [], "source": [ "import stackview\n", "from imageio.v3 import imread\n", "from skimage.filters import gaussian" ] }, { "cell_type": "code", "execution_count": 3, "id": "2ed3eebe-57f2-41aa-9060-48971bde8383", "metadata": { "id": "2ed3eebe-57f2-41aa-9060-48971bde8383" }, "outputs": [], "source": [ "# Activate widgets in google colab\n", "from google.colab import output\n", "output.enable_custom_widget_manager()" ] }, { "cell_type": "markdown", "id": "b9f91fcf-243b-4b8d-af0b-29c4649907c4", "metadata": { "id": "b9f91fcf-243b-4b8d-af0b-29c4649907c4" }, "source": [ "Starting point is a 3D image dataset provided as numpy array." ] }, { "cell_type": "code", "execution_count": 4, "id": "2f21ee1d", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "2f21ee1d", "outputId": "d68b526c-b93c-4676-dc66-4708dd734a15", "tags": [] }, "outputs": [ { "output_type": "execute_result", "data": { "text/plain": [ "(120, 160, 160)" ] }, "metadata": {}, "execution_count": 4 } ], "source": [ "image_stack = imread('https://github.com/clEsperanto/clesperanto_example_data/raw/main/Haase_MRT_tfl3d1.tif?raw=true')\n", "\n", "image_stack.shape" ] }, { "cell_type": "code", "source": [ "stackview.insight(image_stack)" ], "metadata": { "id": "nR8_tHTyymyu", "outputId": "e3b9d1ca-9019-4e75-a489-4d51f97a97de", "colab": { "base_uri": "https://localhost:8080/", "height": 507 } }, "id": "nR8_tHTyymyu", "execution_count": 5, "outputs": [ { "output_type": "display_data", "data": { "text/plain": [ "" ], "text/html": [ "\n", "\n", "\n", "\n", "\n", "
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
shape(120, 160, 160)
dtypeuint16
size5.9 MB
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max65535
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