Execution from folder

.gitignore

@@ -82,58 +82,6 @@ venv/
 
 # written by setuptools_scm
 **/_version.py
-demo/crops/2021-5-7_wt_72hpf_lysosensor_1.czi
-demo/crops/2022-8-19 et358 pnp4a gRNA 72hpf 1.czi
-demo/crops/Crop vs. CZI file.ipynb
-demo/delete/3. Merge individual images to stack.ipynb
-demo/imgs/1. mutant images/img2_20220520_mutant_56hpf_2.tif
-demo/imgs/1. mutant images/img3_l3_20220520_mutant_56hpf_3.tif
-demo/imgs/1. mutant images/img3_l5_20220520_mutant_56hpf_3.tif
-demo/imgs/1. mutant images/img4_l2_20220520_mutant_56hpf_4.tif
-demo/imgs/1. mutant images/img4_l4_20220520_mutant_56hpf_4.tif
-demo/imgs/1. mutant images/img5_l1_20220520_mutant_56hpf_5.tif
-demo/imgs/2. normalized images/img2_20220520_mutant_56hpf_2.tif
-demo/imgs/2. normalized images/img3_l3_20220520_mutant_56hpf_3.tif
-demo/imgs/2. normalized images/img3_l5_20220520_mutant_56hpf_3.tif
-demo/imgs/2. normalized images/img4_l2_20220520_mutant_56hpf_4.tif
-demo/imgs/2. normalized images/img4_l4_20220520_mutant_56hpf_4.tif
-demo/imgs/2. normalized images/img5_l1_20220520_mutant_56hpf_5.tif
-demo/imgs/3. segmentation labels/img2_20220520_mutant_56hpf_2.tif
-demo/imgs/3. segmentation labels/img3_l3_20220520_mutant_56hpf_3.tif
-demo/imgs/3. segmentation labels/img3_l5_20220520_mutant_56hpf_3.tif
-demo/imgs/3. segmentation labels/img4_l2_20220520_mutant_56hpf_4.tif
-demo/imgs/3. segmentation labels/img4_l4_20220520_mutant_56hpf_4.tif
-demo/imgs/3. segmentation labels/img5_l1_20220520_mutant_56hpf_5.tif
-demo/imgs/4. dataframes of segmentation labels/img2_20220520_mutant_56hpf_2.tif.csv
-demo/imgs/4. dataframes of segmentation labels/img3_l3_20220520_mutant_56hpf_3.tif.csv
-demo/imgs/4. dataframes of segmentation labels/img3_l5_20220520_mutant_56hpf_3.tif.csv
-demo/imgs/4. dataframes of segmentation labels/img4_l2_20220520_mutant_56hpf_4.tif.csv
-demo/imgs/4. dataframes of segmentation labels/img4_l4_20220520_mutant_56hpf_4.tif.csv
-demo/imgs/4. dataframes of segmentation labels/img5_l1_20220520_mutant_56hpf_5.tif.csv
-demo/imgs/5. classification labels/img2_20220520_mutant_56hpf_2.tif
-demo/imgs/5. classification labels/img3_l3_20220520_mutant_56hpf_3.tif
-demo/imgs/5. classification labels/img3_l5_20220520_mutant_56hpf_3.tif
-demo/imgs/5. classification labels/img4_l2_20220520_mutant_56hpf_4.tif
-demo/imgs/5. classification labels/img4_l4_20220520_mutant_56hpf_4.tif
-demo/imgs/5. classification labels/img5_l1_20220520_mutant_56hpf_5.tif
-demo/imgs/6. bad-label-excluded labels/img2_20220520_mutant_56hpf_2.tif
-demo/imgs/6. bad-label-excluded labels/img3_l3_20220520_mutant_56hpf_3.tif
-demo/imgs/6. bad-label-excluded labels/img3_l5_20220520_mutant_56hpf_3.tif
-demo/imgs/6. bad-label-excluded labels/img4_l2_20220520_mutant_56hpf_4.tif
-demo/imgs/6. bad-label-excluded labels/img4_l4_20220520_mutant_56hpf_4.tif
-demo/imgs/6. bad-label-excluded labels/img5_l1_20220520_mutant_56hpf_5.tif
-demo/imgs/7. dataframes of DL/img2_20220520_mutant_56hpf_2.tif.csv
-demo/imgs/7. dataframes of DL/img3_l3_20220520_mutant_56hpf_3.tif.csv
-demo/imgs/7. dataframes of DL/img3_l5_20220520_mutant_56hpf_3.tif.csv
-demo/imgs/7. dataframes of DL/img4_l2_20220520_mutant_56hpf_4.tif.csv
-demo/imgs/7. dataframes of DL/img4_l4_20220520_mutant_56hpf_4.tif.csv
-demo/imgs/7. dataframes of DL/img5_l1_20220520_mutant_56hpf_5.tif.csv
-demo/imgs/7. dataframes of PL/img2_20220520_mutant_56hpf_2.tif.csv
-demo/imgs/7. dataframes of PL/img3_l3_20220520_mutant_56hpf_3.tif.csv
-demo/imgs/7. dataframes of PL/img3_l5_20220520_mutant_56hpf_3.tif.csv
-demo/imgs/7. dataframes of PL/img4_l2_20220520_mutant_56hpf_4.tif.csv
-demo/imgs/7. dataframes of PL/img4_l4_20220520_mutant_56hpf_4.tif.csv
-demo/imgs/7. dataframes of PL/img5_l1_20220520_mutant_56hpf_5.tif.csv
-demo/imgs/df_PL.csv
-img/img06_20220513_ET358_56hpf_2.tif
-img/img06_20220513_ET358_56hpf_2.tif
+*.tif
+*.csv
+*.czi

demo/1. Working with czi-files.ipynb

@@ -0,0 +1,178 @@
+{
+ "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
+}