merge to main

timelapse 11 jan 2022.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "2ae2bab7-a76d-489a-82db-541b3b35998d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from droplet_growth import multiwell\n",
+    "import tifffile as tf"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "a31037f7-f7f7-4523-876a-806d0cf4e799",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "big_labels = tf.imread('Y:/Lena/Data/labels_bin2+100.tif')\n",
+    "template16 = tf.imread('Y:/Lena/Data/20210518_control/template_bin16_bf_mask.tif')[0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "740a2dde-a75e-402e-b4a3-056d230b56ef",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mean_proj = tf.imread('Y:Lena/Data//20220111-MIC-resistant/timelapse-30min/0ng-TRITC-19h_meanIP.tif')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "73d33d14-935a-4430-9640-864d25d9d70a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "aligned_meanIP = register.align_timelapse(bf[0,0,0], mean_proj[:,0], template16=template16, mask2=big_labels, binnings=(2,16,2))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1797f6de-4e51-4da9-86f2-0e5bf411e491",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fluo = np.array(aligned_meanIP[1]).reshape((39, 1, 1, 6544, 20896))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e21e05be-06b4-4889-814c-e701b9f0180a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fluo.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f52b459a-c3db-423c-a53b-d54a2b64f6a2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "labels = tf.imread('Y:/Lena/Data/20220111-MIC-resistant/timelapse-30min/lables.tif')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "31849d84-0452-4db2-b1d1-873e42ca4353",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "intensities = multiwell.get_intensity_table(labelled_mask=labels.astype('int'), intensity_image_sequence=fluo[:,0,0])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "84defb2a-71b0-47b6-b44e-82053d030675",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "intensities.loc[:, 'h'] = intensities.time * .5"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "35aca943-50f6-48fb-92fe-55163b6105d7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "intensities.to_csv(\"Y:Lena/Data/20220111-MIC-resistant/timelapse-30min/intesities.csv\", index=None)"
+   ]
+  }
+ ],
+ "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": "3.8.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}