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| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "bd8803c6-ba71-44c0-a009-20e0dd6627ef", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# 1. Working with czi-files" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 1, | ||
| "id": "102fccdb-71e4-40ec-a8bd-d505cf0826b5", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "<Intel(R) UHD Graphics 620 on Platform: Intel(R) OpenCL HD Graphics (1 refs)>" | ||
| ] | ||
| }, | ||
| "execution_count": 1, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "import os\n", | ||
| "import pyclesperanto_prototype as cle\n", | ||
| "import napari\n", | ||
| "from aicsimageio import AICSImage\n", | ||
| "from aicsimageio.readers import BioformatsReader\n", | ||
| "\n", | ||
| "cle.select_device(\"Intel(R) Iris(TM) Plus Graphics 640\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 2, | ||
| "id": "cafd56ae-6051-48f6-8de6-dcc59fd45071", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "image_folder = 'crops/'\n", | ||
| "tif_folder = 'crops/tif-files/'" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "id": "de607dcb-a0a8-4d53-8f85-ab61d7944558", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "os.makedirs(tif_folder, exist_ok=True)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 4, | ||
| "id": "8962be97-6f36-49ae-bb10-9ec3f5718bee", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "data": { | ||
| "text/plain": [ | ||
| "['.ipynb_checkpoints',\n", | ||
| " '2021-5-7_wt_72hpf_lysosensor_1.czi',\n", | ||
| " '2022-8-19 et358 pnp4a gRNA 72hpf 1.czi',\n", | ||
| " 'Crop vs. CZI file.ipynb',\n", | ||
| " 'tif-files']" | ||
| ] | ||
| }, | ||
| "execution_count": 4, | ||
| "metadata": {}, | ||
| "output_type": "execute_result" | ||
| } | ||
| ], | ||
| "source": [ | ||
| "file_list = os.listdir(image_folder)\n", | ||
| "file_list" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 5, | ||
| "id": "6885ae59-9bbe-486b-828f-d2fe192ea8e2", | ||
| "metadata": {}, | ||
| "outputs": [ | ||
| { | ||
| "name": "stderr", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "WARNING: QWindowsWindow::setGeometry: Unable to set geometry 1090x686+7+31 (frame: 1108x733-2-7) on QWidgetWindow/\"_QtMainWindowClassWindow\" on \"\\\\.\\DISPLAY1\". Resulting geometry: 1365x859+8+38 (frame: 1383x906-1+0) margins: 9, 38, 9, 9 minimum size: 612x589 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=630,636 maxtrack=0,0)\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "viewer = napari.Viewer()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 6, | ||
| "id": "bbf5cbe3-8f26-4253-83dc-73f7f7f3db6c", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "def data_selection(filename, image_folder, viewer, channel):\n", | ||
| " '''\n", | ||
| " this function loads one channel of an image slice by slice in napari\n", | ||
| " '''\n", | ||
| " \n", | ||
| " from aicsimageio import AICSImage\n", | ||
| " from aicsimageio.readers import BioformatsReader\n", | ||
| " \n", | ||
| " #load image\n", | ||
| " image = AICSImage(image_folder + filename, reader = BioformatsReader)\n", | ||
| " original = image.data\n", | ||
| " \n", | ||
| " #select reflection channel\n", | ||
| " channel_specified = original[0, channel]\n", | ||
| " \n", | ||
| " #add every slice of the stack to napari\n", | ||
| " for slc in range(channel_specified.shape[0]):\n", | ||
| " layer = viewer.add_image(channel_specified[slc], colormap = 'cyan', blending = 'translucent')" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "d3b2dd75-2ac4-42ac-b5da-dbe012aac151", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Now you can say which image inside the `file_list` you want to display in napari. When you just say `filename = file_list`, you will open all images slice by slice." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 7, | ||
| "id": "4bfb64ab-e5b7-4e03-bf78-07d463811f39", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "data_selection(filename=file_list[2], image_folder=image_folder, viewer=viewer, channel = 2)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "ad37d69b-4b9e-4f40-8840-449ee4b56662", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "You can save the slices of the stack you want to keep under File -> Save Selected Layer(s) (Shortcut: `Ctrl + S`) and direct into the tif_folder" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3 (ipykernel)", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.9.15" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |
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demo/2. Executing guanine-crystal-analysis-plugin from a jupyter notebook.ipynb
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