Spex_workflow.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Segmentation Modules for SPEX Pipeline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Functions for image preproessing, segmentation, and feature extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "INFO:tensorflow:Enabling eager execution\n",
      "INFO:tensorflow:Enabling v2 tensorshape\n",
      "INFO:tensorflow:Enabling resource variables\n",
      "INFO:tensorflow:Enabling tensor equality\n",
      "INFO:tensorflow:Enabling control flow v2\n",
      "2021-07-08 14:37:35,761 [INFO] WRITING LOG OUTPUT TO /gstore/home/jesudasr/.cellpose/run.log\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "optimizer_v2.py (374): The `lr` argument is deprecated, use `learning_rate` instead.\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "import glob\n",
    "import numpy as np\n",
    "from skimage import segmentation\n",
    "from tifffile import TiffWriter, TiffFile\n",
    "\n",
    "import spex_segment as sp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "os.chdir('/gne/data/pathology/t3imagedata/Projects/H2020-428/Images/PAC0002_KerenMIBI/Converted')\n",
    "img='TA459_multipleCores2_Run-4_Point1.tiff'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 1: Load image and extract channels as a list\n",
    "##### (or use OMERO api to pull tiff image and channel names)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Image loaded with the following 44 channels: ['Au', 'Background', 'Beta catenin', 'Ca', 'CD11b', 'CD11c', 'CD138', 'CD16', 'CD20', 'CD209', 'CD3', 'CD31', 'CD4', 'CD45', 'CD45RO', 'CD56', 'CD63', 'CD68', 'CD8', 'dsDNA', 'EGFR', 'Fe', 'FoxP3', 'H3K27me3', 'H3K9ac', 'HLA-DR', 'HLA_Class_1', 'IDO', 'Keratin17', 'Keratin6', 'Ki67', 'Lag3', 'MPO', 'Na', 'P', 'p53', 'Pan-Keratin', 'PD-L1', 'PD1', 'phospho-S6', 'Si', 'SMA', 'Ta', 'Vimentin']\n"
     ]
    }
   ],
   "source": [
    "Image, channel=sp.load_tiff(img,is_mibi=True)\n",
    "\n",
    "print(\"Image loaded with the following\",len(channel),\"channels:\",channel)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 2: Image preprocessing\n",
    "##### These modules are optional. User will select what functions they want to chain together"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### OPTIONAL - Subtract Background noise"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "index=channel.index('Au')\n",
    "bgcorrect_Image=sp.background_subtract(Image, index, 10,2)\n",
    "\n",
    "index=channel.index('Background')\n",
    "bgcorrect_Image=sp.background_subtract(bgcorrect_Image, index, 10,2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### OPTIONAL - NLM Denoising"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "nlm_Image=sp.nlm_denoise(bgcorrect_Image,5,6)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### OPTIONAL - Median filter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "list=['dsDNA','H3K9ac','H3K27me3']\n",
    "\n",
    "to_denoise=[]      \n",
    "for i in range(0,len(list),1):\n",
    "    index=channel.index(list[i])\n",
    "    to_denoise.append(index)\n",
    "to_denoise.sort()\n",
    "\n",
    "median_Image=sp.median_denoise(Image,4,to_denoise)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 3: Cell Segmentation\n",
    "##### User will select 1 of the 3 segmentation options. Output will be a label image where each cell is assigned an integer value."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### StarDist deep learning segmentation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n"
     ]
    }
   ],
   "source": [
    "list=['dsDNA','H3K9ac','H3K27me3']\n",
    "\n",
    "to_merge=[]      \n",
    "for i in range(0,len(list),1):\n",
    "    index=channel.index(list[i])\n",
    "    to_merge.append(index)\n",
    "to_merge.sort()\n",
    "\n",
    "stardist_label=sp.stardist_cellseg(median_Image, to_merge, 1, 0.5, 1, 98.5)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### OR Cellpose deep learning segmentation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2021-07-08 14:38:54,669 [INFO] >>>> using CPU\n",
      "2021-07-08 14:38:56,165 [INFO] ~~~ FINDING MASKS ~~~\n",
      "2021-07-08 14:42:06,196 [INFO] >>>> TOTAL TIME 190.03 sec\n"
     ]
    }
   ],
   "source": [
    "list=['dsDNA','H3K9ac','H3K27me3']\n",
    "\n",
    "to_merge=[]      \n",
    "for i in range(0,len(list),1):\n",
    "    index=channel.index(list[i])\n",
    "    to_merge.append(index)\n",
    "to_merge.sort()\n",
    "\n",
    "cellpose_label=sp.cellpose_cellseg(median_Image, to_merge,12, 1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### OR DeepCell deep learning segmentation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:00:18,118 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:00:26,186 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    }
   ],
   "source": [
    "list=['dsDNA','H3K9ac','H3K27me3']\n",
    "\n",
    "to_merge=[]      \n",
    "for i in range(0,len(list),1):\n",
    "    index=channel.index(list[i])\n",
    "    to_merge.append(index)\n",
    "to_merge.sort()\n",
    "\n",
    "deepcell_label=sp.deepcell_segmentation(Image, to_merge, 0.39)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### OR Classic watershed segmentation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "list=['dsDNA','H3K9ac','H3K27me3']\n",
    "\n",
    "to_merge=[]      \n",
    "for i in range(0,len(list),1):\n",
    "    index=channel.index(list[i])\n",
    "    to_merge.append(index)\n",
    "to_merge.sort()\n",
    "\n",
    "classic_label=sp.classicwatershed_cellseg(median_Image, to_merge)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 4: Postprocessing\n",
    "##### These modules are optional. User will select what functions they want to chain together"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Rescue cells missed by DL model. (uses traditional watershed) - This is an optional step to add after segmentatio step."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "list=['dsDNA','H3K9ac','H3K27me3']\n",
    "\n",
    "to_merge=[]      \n",
    "for i in range(0,len(list),1):\n",
    "    index=channel.index(list[i])\n",
    "    to_merge.append(index)\n",
    "to_merge.sort()\n",
    "\n",
    "new_label=sp.rescue_cells(Image,to_merge, stardist_label)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Remove small and/or large segments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "newlabel=sp.remove_small_objects(new_label, 8)\n",
    "newlabel=sp.remove_large_objects(new_label, 75)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Dilate nuclei boundaries to simulate a cell"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "expanded_label=sp.simulate_cell(deepcell_label, 10)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Step 5: Feature Extraction"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "##### Extract features to be passed to the phenotyping modules"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df=sp.feature_extraction(Image, expanded_label,channel)\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Example Batch Process\n",
    "##### Running a folder of images through the SPEX pipeline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['TA459_multipleCores2_Run-4_Point31.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point38.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point26.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point32.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point37.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point6.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point41.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point24.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point30.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point3.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point12.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point28.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point25.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point18.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point40.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point17.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point29.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point15.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point34.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point22.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point16.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point1.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point9.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point36.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point20.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point23.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point4.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point27.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point33.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point10.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point35.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point39.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point5.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point11.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point19.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point14.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point21.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point8.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point7.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point13.tiff',\n",
       " 'TA459_multipleCores2_Run-4_Point2.tiff']"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "os.chdir('/gne/data/pathology/t3imagedata/Projects/H2020-428/Images/PAC0002_KerenMIBI/Converted')\n",
    "files = glob.glob('*.tiff', recursive = False)\n",
    "files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:24:28,077 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:24:37,067 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:25:57,597 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:26:05,914 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:27:24,279 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:27:32,900 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:29:13,277 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:29:21,346 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:30:56,117 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:31:04,284 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:32:45,071 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:32:53,366 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:34:30,281 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:34:38,809 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:36:18,911 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:36:27,709 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:37:56,021 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:38:04,073 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:40:01,612 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:40:10,095 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:41:50,793 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:41:59,477 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:43:40,726 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:43:48,873 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:45:26,309 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:45:35,001 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:46:49,814 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:46:58,323 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:48:27,847 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:48:36,103 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:50:01,378 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:50:09,554 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:51:55,614 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:52:03,833 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:53:27,576 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:53:36,546 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:54:53,414 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:55:02,343 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:56:38,693 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:56:47,629 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 15:58:16,822 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 15:58:24,660 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:00:12,417 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:00:21,180 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:01:54,715 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:02:03,080 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:03:37,441 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:03:46,152 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:05:05,055 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:05:13,321 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:06:39,800 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:06:48,013 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:08:09,315 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:08:17,835 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:09:57,168 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:10:05,499 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:11:25,823 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:11:33,969 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:12:50,981 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:12:59,643 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:14:33,172 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:14:40,948 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:16:33,993 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:16:42,614 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:18:13,051 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:18:21,519 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:19:55,564 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:20:03,508 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:21:32,844 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:21:41,745 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:23:06,122 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:23:14,386 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:24:48,968 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:24:57,221 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:26:28,406 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:26:37,248 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:28:00,787 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:28:08,719 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:29:35,980 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:29:44,174 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found model '2D_versatile_fluo' for 'StarDist2D'.\n",
      "Loading network weights from 'weights_best.h5'.\n",
      "Loading thresholds from 'thresholds.json'.\n",
      "Using default values: prob_thresh=0.479071, nms_thresh=0.3.\n",
      "WARNING:tensorflow:SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "2021-07-08 16:31:28,152 [WARNING] SavedModel saved prior to TF 2.5 detected when loading Keras model. Please ensure that you are saving the model with model.save() or tf.keras.models.save_model(), *NOT* tf.saved_model.save(). To confirm, there should be a file named \"keras_metadata.pb\" in the SavedModel directory.\n",
      "WARNING:tensorflow:No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n",
      "2021-07-08 16:31:36,740 [WARNING] No training configuration found in save file, so the model was *not* compiled. Compile it manually.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "spex_segment.py (413): indices argument is deprecated and will be removed in version 0.20. To avoid this warning, please do not use the indices argument. Please see peak_local_max documentation for more details.\n"
     ]
    }
   ],
   "source": [
    "for image in files:\n",
    "    #Load Image\n",
    "    Image, channel=sp.load_tiff(image,is_mibi=True)\n",
    "\n",
    "    #Denoise Image\n",
    "    list=['dsDNA','H3K9ac','H3K27me3']\n",
    "\n",
    "    to_denoise=[]      \n",
    "    for i in range(0,len(list),1):\n",
    "        index=channel.index(list[i])\n",
    "        to_denoise.append(index)\n",
    "    to_denoise.sort()\n",
    "\n",
    "    median_Image=sp.median_denoise(Image,5,to_denoise)\n",
    "\n",
    "    #Run Segmentation\n",
    "    list=['dsDNA','H3K9ac','H3K27me3']\n",
    "\n",
    "    to_merge=[]      \n",
    "    for i in range(0,len(list),1):\n",
    "        index=channel.index(list[i])\n",
    "        to_merge.append(index)\n",
    "    to_merge.sort()\n",
    "    \n",
    "    stardist_label=sp.stardist_cellseg(median_Image, to_merge, 1, 0.5, 1, 98.5)\n",
    "    #cellpose_label=sp.cellpose_cellseg(median_Image, index,12, 1)\n",
    "    deepcell_label=sp.deepcell_segmentation(Image, to_merge, 0.39)\n",
    "\n",
    "    #index=channel.index('H3K27me3')\n",
    "    new_label=sp.rescue_cells(Image,to_merge, stardist_label)\n",
    "    #new_label2=sp.rescue_cells(Image,index, cellpose_label)\n",
    "    #new_label3=sp.rescue_cells(Image,index, deepcell_label)\n",
    "\n",
    "    #Dilate Cells\n",
    "    expanded_label=sp.simulate_cell(new_label, 10)\n",
    "    #expanded_label2=sp.simulate_cell(new_label2, 10)\n",
    "    expanded_label3=sp.simulate_cell(deepcell_label, 8)\n",
    "\n",
    "    #Extract Features\n",
    "    df=sp.feature_extraction(Image, expanded_label,channel)\n",
    "    df2=sp.feature_extraction(Image, expanded_label3,channel)\n",
    "\n",
    "    #Save Feature Data\n",
    "    csvname = image.split(\".tiff\")[0]+'_stardist.csv'\n",
    "    df.to_csv(csvname, index = False)\n",
    "    csvname = image.split(\".tiff\")[0]+'_deepcell.csv'\n",
    "    df2.to_csv(csvname, index = False)\n",
    "\n",
    "    #Save Image of segmentation\n",
    "    imagename = image.split(\".tiff\")[0]+'_label.ome.tiff'\n",
    "\n",
    "    contour=segmentation.find_boundaries(expanded_label, connectivity=1, mode='thick', background=0)\n",
    "    #contour2=segmentation.find_boundaries(expanded_label2, connectivity=1, mode='thick', background=0)\n",
    "    contour3=segmentation.find_boundaries(expanded_label3, connectivity=1, mode='thick', background=0)\n",
    "    pseudoIF=np.stack((Image[channel.index('dsDNA')],Image[channel.index('H3K9ac')],Image[channel.index('H3K27me3')],contour,contour3), axis=0)\n",
    "\n",
    "    with TiffWriter(imagename, bigtiff=True) as tif:\n",
    "        options = dict(tile=(512, 512),photometric='minisblack')\n",
    "        tif.write(pseudoIF, **options, metadata={'PhysicalSizeX':0.39,'PhysicalSizeY':0.39,'Channel': {'Name': [\"dsDNA\",\"H3K9ac\",\"H3K27me3\", \"Stardist\",\"DeepCell\"]}})"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python (spex)",
   "language": "python",
   "name": "spex_dev"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.4"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}