From 39ea45789077b21560bb7db1e206618c7f43e035 Mon Sep 17 00:00:00 2001
From: Jonas Windhager <jonas.windhager@uzh.ch>
Date: Sun, 10 Apr 2022 19:28:58 +0200
Subject: [PATCH 1/6] sort analysis stack channels by mass (closes #88)

---
 scripts/imc_preprocessing.ipynb | 20 +++++++++++++-------
 scripts/imc_preprocessing.py    | 16 +++++++++++-----
 src/imcsegpipe/__init__.py      | 13 ++++++-------
 src/imcsegpipe/_imcsegpipe.py   | 16 ++++++++--------
 src/imcsegpipe/utils.py         | 13 +++++++++----
 5 files changed, 47 insertions(+), 31 deletions(-)

diff --git a/scripts/imc_preprocessing.ipynb b/scripts/imc_preprocessing.ipynb
index 66ef105..f2d51bb 100755
--- a/scripts/imc_preprocessing.ipynb
+++ b/scripts/imc_preprocessing.ipynb
@@ -16,18 +16,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 1,
    "id": "70edc343",
    "metadata": {},
    "outputs": [],
    "source": [
-    "import imcsegpipe\n",
-    "import pandas as pd\n",
     "import shutil\n",
-    "\n",
     "from pathlib import Path\n",
     "from tempfile import TemporaryDirectory\n",
-    "from typing import List"
+    "from typing import List\n",
+    "\n",
+    "import pandas as pd\n",
+    "\n",
+    "import imcsegpipe\n",
+    "from imcsegpipe.utils import sort_channels_by_mass"
    ]
   },
   {
@@ -316,7 +318,9 @@
     "        imcsegpipe.create_analysis_stacks(\n",
     "            acquisition_dir=acquisition_dir,\n",
     "            analysis_dir=final_images_dir,\n",
-    "            analysis_channels=panel.loc[panel[panel_keep_col] == 1, panel_channel_col].tolist(),\n",
+    "            analysis_channels=sort_channels_by_mass(\n",
+    "                panel.loc[panel[panel_keep_col] == 1, panel_channel_col].tolist()\n",
+    "            ),\n",
     "            suffix=\"_full\",\n",
     "            hpf=50.0,\n",
     "        )\n",
@@ -324,7 +328,9 @@
     "        imcsegpipe.create_analysis_stacks(\n",
     "            acquisition_dir=acquisition_dir,\n",
     "            analysis_dir=ilastik_dir,\n",
-    "            analysis_channels=panel.loc[panel[panel_ilastik_col] == 1, panel_channel_col].tolist(),\n",
+    "            analysis_channels=sort_channels_by_mass(\n",
+    "                panel.loc[panel[panel_ilastik_col] == 1, panel_channel_col].tolist()\n",
+    "            ),\n",
     "            suffix=\"_ilastik\",\n",
     "            hpf=50.0,\n",
     "        )"
diff --git a/scripts/imc_preprocessing.py b/scripts/imc_preprocessing.py
index d31270c..29218ba 100644
--- a/scripts/imc_preprocessing.py
+++ b/scripts/imc_preprocessing.py
@@ -6,14 +6,16 @@
 # !{sys.executable} -m pip install -e {Path.cwd().parent}
 
 # %%
-import imcsegpipe
-import pandas as pd
 import shutil
-
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from typing import List
 
+import pandas as pd
+
+import imcsegpipe
+from imcsegpipe.utils import sort_channels_by_mass
+
 # %% [markdown]
 #
 # # Preprocessing of IMC data for image segmentation
@@ -197,7 +199,9 @@
         imcsegpipe.create_analysis_stacks(
             acquisition_dir=acquisition_dir,
             analysis_dir=final_images_dir,
-            analysis_channels=panel.loc[panel[panel_keep_col] == 1, panel_channel_col].tolist(),
+            analysis_channels=sort_channels_by_mass(
+                panel.loc[panel[panel_keep_col] == 1, panel_channel_col].tolist()
+            ),
             suffix="_full",
             hpf=50.0,
         )
@@ -205,7 +209,9 @@
         imcsegpipe.create_analysis_stacks(
             acquisition_dir=acquisition_dir,
             analysis_dir=ilastik_dir,
-            analysis_channels=panel.loc[panel[panel_ilastik_col] == 1, panel_channel_col].tolist(),
+            analysis_channels=sort_channels_by_mass(
+                panel.loc[panel[panel_ilastik_col] == 1, panel_channel_col].tolist()
+            ),
             suffix="_ilastik",
             hpf=50.0,
         )
diff --git a/src/imcsegpipe/__init__.py b/src/imcsegpipe/__init__.py
index f2fd224..1bef2ed 100644
--- a/src/imcsegpipe/__init__.py
+++ b/src/imcsegpipe/__init__.py
@@ -1,16 +1,15 @@
 from ._imcsegpipe import (
-    extract_zip_file,
-    match_txt_files,
-    extract_mcd_file,
     create_analysis_stacks,
     export_to_histocat,
+    extract_mcd_file,
+    extract_zip_file,
+    match_txt_files,
 )
 
-
 __all__ = [
-    "extract_zip_file",
-    "match_txt_files",
-    "extract_mcd_file",
     "create_analysis_stacks",
     "export_to_histocat",
+    "extract_mcd_file",
+    "extract_zip_file",
+    "match_txt_files",
 ]
diff --git a/src/imcsegpipe/_imcsegpipe.py b/src/imcsegpipe/_imcsegpipe.py
index 15a1a6d..81c53cb 100644
--- a/src/imcsegpipe/_imcsegpipe.py
+++ b/src/imcsegpipe/_imcsegpipe.py
@@ -1,19 +1,19 @@
-import imageio
 import logging
-import numpy as np
-import pandas as pd
 import re
 import shutil
-import tifffile
-import xtiff
-
 from os import PathLike
 from pathlib import Path
-from readimc import MCDFile, TXTFile
-from readimc.data import Acquisition, Panorama, Slide
 from typing import Dict, List, Optional, Sequence, Union
 from zipfile import ZipFile
 
+import imageio
+import numpy as np
+import pandas as pd
+import tifffile
+import xtiff
+from readimc import MCDFile, TXTFile
+from readimc.data import Acquisition, Panorama, Slide
+
 from .utils import AcquisitionMetadata, filter_hot_pixels, get_acquisition_ome_xml
 
 
diff --git a/src/imcsegpipe/utils.py b/src/imcsegpipe/utils.py
index 33fc3b1..c4eac04 100644
--- a/src/imcsegpipe/utils.py
+++ b/src/imcsegpipe/utils.py
@@ -1,12 +1,13 @@
+import re
+from dataclasses import dataclass
+from typing import List, Optional, Sequence
+from xml.etree import ElementTree as ET
+
 import numpy as np
 import xtiff
-
-from dataclasses import dataclass
 from readimc import MCDFile
 from readimc.data import Acquisition
 from scipy.ndimage import maximum_filter
-from typing import Optional, Sequence
-from xml.etree import ElementTree as ET
 
 
 @dataclass
@@ -156,3 +157,7 @@ def filter_hot_pixels(img: np.ndarray, thres: float) -> np.ndarray:
     kernel[0, 1, 1] = False
     max_neighbor_img = maximum_filter(img, footprint=kernel, mode="mirror")
     return np.where(img - max_neighbor_img > thres, max_neighbor_img, img)
+
+
+def sort_channels_by_mass(channels: Sequence[str]) -> List[str]:
+    return sorted(channels, lambda channel: int(re.sub("[^0-9]", "", channel) or 0))

From 6f8e0623700c777136eb59d69e29884e378bae1a Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Mon, 11 Apr 2022 15:47:27 +0200
Subject: [PATCH 2/6] Added link to newest classifier

---
 scripts/download_examples.ipynb | 156 +++++++++++++++++---------------
 scripts/download_examples.py    |   4 +-
 2 files changed, 85 insertions(+), 75 deletions(-)

diff --git a/scripts/download_examples.ipynb b/scripts/download_examples.ipynb
index 7df7382..8c0bb3f 100644
--- a/scripts/download_examples.ipynb
+++ b/scripts/download_examples.ipynb
@@ -60,7 +60,7 @@
     "# Ilastik project\n",
     "ilastik_project = Path(\"..\") / \"IMCWorkflow.ilp\"\n",
     "if not ilastik_project.exists():\n",
-    "    request.urlretrieve(\"https://zenodo.org/record/6043544/files/IMCWorkflow.ilp\", ilastik_project)\n",
+    "    request.urlretrieve(\"https://zenodo.org/record/6404960/files/IMCWorkflow.ilp\", ilastik_project)\n",
     "    \n",
     "# Sample metadata\n",
     "sample_metadata = Path(\"..\") / \"sample_metadata.xlsx\"\n",
@@ -70,7 +70,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "5cebbf89",
    "metadata": {},
    "outputs": [
@@ -82,134 +82,142 @@
       "#\n",
       "# Name                    Version                   Build  Channel\n",
       "anyio                     3.5.0            py39h6e9494a_0    conda-forge\n",
-      "appnope                   0.1.2            py39h6e9494a_2    conda-forge\n",
+      "appnope                   0.1.3              pyhd8ed1ab_0    conda-forge\n",
       "argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge\n",
-      "argon2-cffi-bindings      21.2.0           py39h89e85a6_1    conda-forge\n",
+      "argon2-cffi-bindings      21.2.0           py39h63b48b0_2    conda-forge\n",
       "asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge\n",
       "attrs                     21.4.0             pyhd8ed1ab_0    conda-forge\n",
       "babel                     2.9.1              pyh44b312d_0    conda-forge\n",
       "backcall                  0.2.0              pyh9f0ad1d_0    conda-forge\n",
       "backports                 1.0                        py_2    conda-forge\n",
       "backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge\n",
-      "black                     22.1.0             pyhd8ed1ab_0    conda-forge\n",
-      "bleach                    4.1.0              pyhd8ed1ab_0    conda-forge\n",
-      "brotlipy                  0.7.0           py39h89e85a6_1003    conda-forge\n",
+      "beautifulsoup4            4.11.1             pyha770c72_0    conda-forge\n",
+      "bleach                    5.0.0              pyhd8ed1ab_0    conda-forge\n",
+      "brotlipy                  0.7.0           py39h63b48b0_1004    conda-forge\n",
       "bzip2                     1.0.8                h0d85af4_4    conda-forge\n",
       "ca-certificates           2021.10.8            h033912b_0    conda-forge\n",
-      "certifi                   2021.10.8        py39h6e9494a_1    conda-forge\n",
+      "certifi                   2021.10.8        py39h6e9494a_2    conda-forge\n",
       "cffi                      1.15.0           py39he338e87_0    conda-forge\n",
-      "charset-normalizer        2.0.11             pyhd8ed1ab_0    conda-forge\n",
-      "click                     8.0.3            py39h6e9494a_1    conda-forge\n",
-      "cryptography              36.0.1           py39h209aa08_0    conda-forge\n",
-      "dataclasses               0.8                pyhc8e2a94_3    conda-forge\n",
-      "debugpy                   1.5.1            py39h9fcab8e_0    conda-forge\n",
+      "charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge\n",
+      "cryptography              36.0.2           py39h1644bb1_1    conda-forge\n",
+      "debugpy                   1.6.0            py39hfd1d529_0    conda-forge\n",
       "decorator                 5.1.1              pyhd8ed1ab_0    conda-forge\n",
       "defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge\n",
       "entrypoints               0.4                pyhd8ed1ab_0    conda-forge\n",
-      "executing                 0.8.2              pyhd8ed1ab_0    conda-forge\n",
-      "flit-core                 3.6.0              pyhd8ed1ab_0    conda-forge\n",
+      "executing                 0.8.3              pyhd8ed1ab_0    conda-forge\n",
+      "flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge\n",
       "idna                      3.3                pyhd8ed1ab_0    conda-forge\n",
-      "imageio                   2.16.0                   pypi_0    pypi\n",
-      "importlib-metadata        4.11.0           py39h6e9494a_0    conda-forge\n",
-      "importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge\n",
-      "ipykernel                 6.9.0            py39h71a6800_0    conda-forge\n",
-      "ipython                   8.0.1            py39h6e9494a_0    conda-forge\n",
+      "imageio                   2.16.2                   pypi_0    pypi\n",
+      "importlib-metadata        4.11.3           py39h6e9494a_1    conda-forge\n",
+      "importlib_resources       5.6.0              pyhd8ed1ab_0    conda-forge\n",
+      "ipykernel                 6.12.1           py39h71a6800_0    conda-forge\n",
+      "ipython                   8.2.0            py39h6e9494a_0    conda-forge\n",
       "ipython_genutils          0.2.0                      py_1    conda-forge\n",
-      "jedi                      0.18.1           py39h6e9494a_0    conda-forge\n",
-      "jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge\n",
+      "jedi                      0.18.1           py39h6e9494a_1    conda-forge\n",
+      "jinja2                    3.1.1              pyhd8ed1ab_0    conda-forge\n",
       "json5                     0.9.5              pyh9f0ad1d_0    conda-forge\n",
       "jsonschema                4.4.0              pyhd8ed1ab_0    conda-forge\n",
-      "jupyter_client            7.1.2              pyhd8ed1ab_0    conda-forge\n",
-      "jupyter_core              4.9.1            py39h6e9494a_1    conda-forge\n",
-      "jupyter_server            1.13.5             pyhd8ed1ab_1    conda-forge\n",
-      "jupyterlab                3.2.9              pyhd8ed1ab_0    conda-forge\n",
-      "jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge\n",
-      "jupyterlab_server         2.10.3             pyhd8ed1ab_0    conda-forge\n",
-      "jupytext                  1.13.6             pyheef035f_0    conda-forge\n",
-      "libcxx                    12.0.1               habf9029_1    conda-forge\n",
+      "jupyter_client            7.2.2              pyhd8ed1ab_1    conda-forge\n",
+      "jupyter_core              4.9.2            py39h6e9494a_0    conda-forge\n",
+      "jupyter_server            1.16.0             pyhd8ed1ab_1    conda-forge\n",
+      "jupyterlab                3.3.3              pyhd8ed1ab_0    conda-forge\n",
+      "jupyterlab_pygments       0.2.0              pyhd8ed1ab_0    conda-forge\n",
+      "jupyterlab_server         2.12.0             pyhd8ed1ab_0    conda-forge\n",
+      "jupytext                  1.13.8             pyh4b9bcc7_0    conda-forge\n",
+      "libcxx                    13.0.1               hc203e6f_0    conda-forge\n",
       "libffi                    3.4.2                h0d85af4_5    conda-forge\n",
       "libsodium                 1.0.18               hbcb3906_1    conda-forge\n",
-      "libzlib                   1.2.11            h9173be1_1013    conda-forge\n",
-      "markdown-it-py            1.1.0              pyhd8ed1ab_0    conda-forge\n",
-      "markupsafe                2.0.1            py39h89e85a6_1    conda-forge\n",
+      "libzlib                   1.2.11            h6c3fc93_1014    conda-forge\n",
+      "markdown-it-py            2.0.1              pyhd8ed1ab_0    conda-forge\n",
+      "markupsafe                2.1.1            py39h63b48b0_1    conda-forge\n",
       "matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge\n",
       "mdit-py-plugins           0.3.0              pyhd8ed1ab_0    conda-forge\n",
+      "mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge\n",
       "mistune                   0.8.4           py39h89e85a6_1005    conda-forge\n",
-      "mypy_extensions           0.4.3            py39h6e9494a_4    conda-forge\n",
-      "nbclassic                 0.3.5              pyhd8ed1ab_0    conda-forge\n",
-      "nbclient                  0.5.10             pyhd8ed1ab_1    conda-forge\n",
-      "nbconvert                 6.4.2            py39h6e9494a_0    conda-forge\n",
-      "nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge\n",
-      "ncurses                   6.3                  he49afe7_0    conda-forge\n",
-      "nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge\n",
-      "notebook                  6.4.8              pyha770c72_0    conda-forge\n",
-      "numpy                     1.22.2                   pypi_0    pypi\n",
-      "openssl                   1.1.1l               h0d85af4_0    conda-forge\n",
+      "nbclassic                 0.3.7              pyhd8ed1ab_0    conda-forge\n",
+      "nbclient                  0.5.13             pyhd8ed1ab_0    conda-forge\n",
+      "nbconvert                 6.4.5              pyhd8ed1ab_2    conda-forge\n",
+      "nbconvert-core            6.4.5              pyhd8ed1ab_2    conda-forge\n",
+      "nbconvert-pandoc          6.4.5              pyhd8ed1ab_2    conda-forge\n",
+      "nbformat                  5.3.0              pyhd8ed1ab_0    conda-forge\n",
+      "ncurses                   6.3                  h96cf925_1    conda-forge\n",
+      "nest-asyncio              1.5.5              pyhd8ed1ab_0    conda-forge\n",
+      "notebook                  6.4.10             pyha770c72_0    conda-forge\n",
+      "notebook-shim             0.1.0              pyhd8ed1ab_0    conda-forge\n",
+      "numpy                     1.22.3                   pypi_0    pypi\n",
+      "openssl                   1.1.1n               h6c3fc93_0    conda-forge\n",
       "packaging                 21.3               pyhd8ed1ab_0    conda-forge\n",
-      "pandas                    1.4.1                    pypi_0    pypi\n",
+      "pandas                    1.4.2                    pypi_0    pypi\n",
       "pandoc                    2.17.1.1             h694c41f_0    conda-forge\n",
       "pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge\n",
       "parso                     0.8.3              pyhd8ed1ab_0    conda-forge\n",
-      "pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge\n",
       "pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge\n",
       "pickleshare               0.7.5                   py_1003    conda-forge\n",
-      "pillow                    9.0.1                    pypi_0    pypi\n",
-      "pip                       22.0.3             pyhd8ed1ab_0    conda-forge\n",
-      "platformdirs              2.5.0              pyhd8ed1ab_0    conda-forge\n",
-      "prometheus_client         0.13.1             pyhd8ed1ab_0    conda-forge\n",
-      "prompt-toolkit            3.0.27             pyha770c72_0    conda-forge\n",
+      "pillow                    9.1.0                    pypi_0    pypi\n",
+      "pip                       22.0.4             pyhd8ed1ab_0    conda-forge\n",
+      "prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge\n",
+      "prompt-toolkit            3.0.29             pyha770c72_0    conda-forge\n",
+      "psutil                    5.9.0            py39h63b48b0_1    conda-forge\n",
       "ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge\n",
       "pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge\n",
       "pycparser                 2.21               pyhd8ed1ab_0    conda-forge\n",
       "pygments                  2.11.2             pyhd8ed1ab_0    conda-forge\n",
       "pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge\n",
-      "pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge\n",
-      "pyrsistent                0.18.1           py39h89e85a6_0    conda-forge\n",
-      "pysocks                   1.7.1            py39h6e9494a_4    conda-forge\n",
-      "python                    3.9.10          h1dd9edd_2_cpython    conda-forge\n",
+      "pyparsing                 3.0.8              pyhd8ed1ab_0    conda-forge\n",
+      "pyrsistent                0.18.1           py39h63b48b0_1    conda-forge\n",
+      "pysocks                   1.7.1            py39h6e9494a_5    conda-forge\n",
+      "python                    3.9.12          h8b4d769_1_cpython    conda-forge\n",
       "python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge\n",
+      "python-fastjsonschema     2.15.3             pyhd8ed1ab_0    conda-forge\n",
       "python_abi                3.9                      2_cp39    conda-forge\n",
-      "pytz                      2021.3             pyhd8ed1ab_0    conda-forge\n",
-      "pyyaml                    6.0              py39h89e85a6_3    conda-forge\n",
-      "pyzmq                     22.3.0           py39h7fec2f1_1    conda-forge\n",
+      "pytz                      2022.1             pyhd8ed1ab_0    conda-forge\n",
+      "pyyaml                    6.0              py39h63b48b0_4    conda-forge\n",
+      "pyzmq                     22.3.0           py39hc2dc7ec_2    conda-forge\n",
       "readimc                   0.6.1                    pypi_0    pypi\n",
       "readline                  8.1                  h05e3726_0    conda-forge\n",
       "requests                  2.27.1             pyhd8ed1ab_0    conda-forge\n",
       "scipy                     1.8.0                    pypi_0    pypi\n",
       "send2trash                1.8.0              pyhd8ed1ab_0    conda-forge\n",
-      "setuptools                60.9.0           py39h6e9494a_0    conda-forge\n",
+      "setuptools                62.1.0           py39h6e9494a_0    conda-forge\n",
       "six                       1.16.0             pyh6c4a22f_0    conda-forge\n",
-      "sniffio                   1.2.0            py39h6e9494a_2    conda-forge\n",
-      "sqlite                    3.37.0               h23a322b_0    conda-forge\n",
-      "stack_data                0.1.4              pyhd8ed1ab_0    conda-forge\n",
-      "terminado                 0.13.1           py39h6e9494a_0    conda-forge\n",
-      "testpath                  0.5.0              pyhd8ed1ab_0    conda-forge\n",
-      "tifffile                  2022.2.9                 pypi_0    pypi\n",
-      "tk                        8.6.11               h5dbffcc_1    conda-forge\n",
+      "sniffio                   1.2.0            py39h6e9494a_3    conda-forge\n",
+      "soupsieve                 2.3.1              pyhd8ed1ab_0    conda-forge\n",
+      "sqlite                    3.37.1               hb516253_0    conda-forge\n",
+      "stack_data                0.2.0              pyhd8ed1ab_0    conda-forge\n",
+      "terminado                 0.13.3           py39h6e9494a_1    conda-forge\n",
+      "testpath                  0.6.0              pyhd8ed1ab_0    conda-forge\n",
+      "tifffile                  2022.4.8                 pypi_0    pypi\n",
+      "tk                        8.6.12               h5dbffcc_0    conda-forge\n",
       "toml                      0.10.2             pyhd8ed1ab_0    conda-forge\n",
-      "tomli                     2.0.1              pyhd8ed1ab_0    conda-forge\n",
-      "tornado                   6.1              py39h89e85a6_2    conda-forge\n",
+      "tornado                   6.1              py39h63b48b0_3    conda-forge\n",
       "traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge\n",
-      "typed-ast                 1.5.2            py39h89e85a6_0    conda-forge\n",
-      "typing_extensions         4.0.1              pyha770c72_0    conda-forge\n",
-      "tzdata                    2021e                he74cb21_0    conda-forge\n",
-      "urllib3                   1.26.8             pyhd8ed1ab_1    conda-forge\n",
+      "typing_extensions         4.1.1              pyha770c72_0    conda-forge\n",
+      "tzdata                    2022a                h191b570_0    conda-forge\n",
+      "urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge\n",
       "wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge\n",
       "webencodings              0.5.1                      py_1    conda-forge\n",
-      "websocket-client          1.2.3              pyhd8ed1ab_0    conda-forge\n",
+      "websocket-client          1.3.2              pyhd8ed1ab_0    conda-forge\n",
       "wheel                     0.37.1             pyhd8ed1ab_0    conda-forge\n",
       "xtiff                     0.7.7                    pypi_0    pypi\n",
       "xz                        5.2.5                haf1e3a3_1    conda-forge\n",
       "yaml                      0.2.5                h0d85af4_2    conda-forge\n",
       "zeromq                    4.3.4                he49afe7_1    conda-forge\n",
-      "zipp                      3.7.0              pyhd8ed1ab_1    conda-forge\n",
-      "zlib                      1.2.11            h9173be1_1013    conda-forge\n"
+      "zipp                      3.8.0              pyhd8ed1ab_0    conda-forge\n",
+      "zlib                      1.2.11            h6c3fc93_1014    conda-forge\n"
      ]
     }
    ],
    "source": [
     "!conda list"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3c208521-9c2e-449e-8652-69a2016c7c88",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
diff --git a/scripts/download_examples.py b/scripts/download_examples.py
index 17439fb..b2f6636 100644
--- a/scripts/download_examples.py
+++ b/scripts/download_examples.py
@@ -43,7 +43,7 @@
 # Ilastik project
 ilastik_project = Path("..") / "IMCWorkflow.ilp"
 if not ilastik_project.exists():
-    request.urlretrieve("https://zenodo.org/record/6043544/files/IMCWorkflow.ilp", ilastik_project)
+    request.urlretrieve("https://zenodo.org/record/6404960/files/IMCWorkflow.ilp", ilastik_project)
     
 # Sample metadata
 sample_metadata = Path("..") / "sample_metadata.xlsx"
@@ -52,3 +52,5 @@
 
 # %%
 # !conda list
+
+# %%

From 281ef1f9c2953f7ca39eeb1eac689d4462669a35 Mon Sep 17 00:00:00 2001
From: Jonas Windhager <jonas.windhager@uzh.ch>
Date: Mon, 11 Apr 2022 15:58:13 +0200
Subject: [PATCH 3/6] Update utils.py

---
 src/imcsegpipe/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/imcsegpipe/utils.py b/src/imcsegpipe/utils.py
index c4eac04..cb8d7ca 100644
--- a/src/imcsegpipe/utils.py
+++ b/src/imcsegpipe/utils.py
@@ -160,4 +160,4 @@ def filter_hot_pixels(img: np.ndarray, thres: float) -> np.ndarray:
 
 
 def sort_channels_by_mass(channels: Sequence[str]) -> List[str]:
-    return sorted(channels, lambda channel: int(re.sub("[^0-9]", "", channel) or 0))
+    return sorted(channels, key=lambda channel: int(re.sub("[^0-9]", "", channel) or 0))

From 9ecb1a39994819275b237056e6595c01830ef452 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Mon, 11 Apr 2022 18:38:20 +0200
Subject: [PATCH 4/6] Reran notebook

---
 scripts/imc_preprocessing.ipynb | 181 +++++++++++++++++---------------
 scripts/imc_preprocessing.py    |   2 +
 2 files changed, 97 insertions(+), 86 deletions(-)

diff --git a/scripts/imc_preprocessing.ipynb b/scripts/imc_preprocessing.ipynb
index f2d51bb..debf429 100755
--- a/scripts/imc_preprocessing.ipynb
+++ b/scripts/imc_preprocessing.ipynb
@@ -11,7 +11,7 @@
     "\n",
     "# from pathlib import Path\n",
     "\n",
-    "# !{sys.executable} -m pip install -e {Path.cwd().parent}"
+    "!{sys.executable} -m pip install -e {Path.cwd().parent}"
    ]
   },
   {
@@ -78,7 +78,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 2,
    "id": "59626637",
    "metadata": {},
    "outputs": [],
@@ -123,7 +123,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 3,
    "id": "281ad642",
    "metadata": {},
    "outputs": [],
@@ -157,7 +157,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 4,
    "id": "0ac63953",
    "metadata": {},
    "outputs": [],
@@ -189,7 +189,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 5,
    "id": "1169391e",
    "metadata": {},
    "outputs": [],
@@ -235,7 +235,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 6,
    "id": "ce4a4040",
    "metadata": {},
    "outputs": [
@@ -245,7 +245,7 @@
        "PosixPath('../analysis/cpout/panel.csv')"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -267,7 +267,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 7,
    "id": "0dc3d319",
    "metadata": {},
    "outputs": [],
@@ -305,7 +305,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 8,
    "id": "320202b6",
    "metadata": {},
    "outputs": [],
@@ -348,7 +348,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 9,
    "id": "ece67368",
    "metadata": {},
    "outputs": [
@@ -358,7 +358,7 @@
        "PosixPath('../analysis/cpinp/full_channelmeta.csv')"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -378,7 +378,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 10,
    "id": "d7a25f2b",
    "metadata": {},
    "outputs": [],
@@ -422,7 +422,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 11,
    "id": "e6cb34d5",
    "metadata": {},
    "outputs": [
@@ -434,134 +434,143 @@
       "#\n",
       "# Name                    Version                   Build  Channel\n",
       "anyio                     3.5.0            py39h6e9494a_0    conda-forge\n",
-      "appnope                   0.1.2            py39h6e9494a_2    conda-forge\n",
+      "appnope                   0.1.3              pyhd8ed1ab_0    conda-forge\n",
       "argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge\n",
-      "argon2-cffi-bindings      21.2.0           py39h89e85a6_1    conda-forge\n",
+      "argon2-cffi-bindings      21.2.0           py39h63b48b0_2    conda-forge\n",
       "asttokens                 2.0.5              pyhd8ed1ab_0    conda-forge\n",
       "attrs                     21.4.0             pyhd8ed1ab_0    conda-forge\n",
       "babel                     2.9.1              pyh44b312d_0    conda-forge\n",
       "backcall                  0.2.0              pyh9f0ad1d_0    conda-forge\n",
       "backports                 1.0                        py_2    conda-forge\n",
       "backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge\n",
-      "black                     22.1.0             pyhd8ed1ab_0    conda-forge\n",
-      "bleach                    4.1.0              pyhd8ed1ab_0    conda-forge\n",
-      "brotlipy                  0.7.0           py39h89e85a6_1003    conda-forge\n",
+      "beautifulsoup4            4.11.1             pyha770c72_0    conda-forge\n",
+      "bleach                    5.0.0              pyhd8ed1ab_0    conda-forge\n",
+      "brotlipy                  0.7.0           py39h63b48b0_1004    conda-forge\n",
       "bzip2                     1.0.8                h0d85af4_4    conda-forge\n",
       "ca-certificates           2021.10.8            h033912b_0    conda-forge\n",
-      "certifi                   2021.10.8        py39h6e9494a_1    conda-forge\n",
+      "certifi                   2021.10.8        py39h6e9494a_2    conda-forge\n",
       "cffi                      1.15.0           py39he338e87_0    conda-forge\n",
-      "charset-normalizer        2.0.11             pyhd8ed1ab_0    conda-forge\n",
-      "click                     8.0.3            py39h6e9494a_1    conda-forge\n",
-      "cryptography              36.0.1           py39h209aa08_0    conda-forge\n",
-      "dataclasses               0.8                pyhc8e2a94_3    conda-forge\n",
-      "debugpy                   1.5.1            py39h9fcab8e_0    conda-forge\n",
+      "charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge\n",
+      "cryptography              36.0.2           py39h1644bb1_1    conda-forge\n",
+      "debugpy                   1.6.0            py39hfd1d529_0    conda-forge\n",
       "decorator                 5.1.1              pyhd8ed1ab_0    conda-forge\n",
       "defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge\n",
       "entrypoints               0.4                pyhd8ed1ab_0    conda-forge\n",
-      "executing                 0.8.2              pyhd8ed1ab_0    conda-forge\n",
-      "flit-core                 3.6.0              pyhd8ed1ab_0    conda-forge\n",
+      "executing                 0.8.3              pyhd8ed1ab_0    conda-forge\n",
+      "flit-core                 3.7.1              pyhd8ed1ab_0    conda-forge\n",
       "idna                      3.3                pyhd8ed1ab_0    conda-forge\n",
-      "imageio                   2.16.0                   pypi_0    pypi\n",
-      "importlib-metadata        4.11.0           py39h6e9494a_0    conda-forge\n",
-      "importlib_resources       5.4.0              pyhd8ed1ab_0    conda-forge\n",
-      "ipykernel                 6.9.0            py39h71a6800_0    conda-forge\n",
-      "ipython                   8.0.1            py39h6e9494a_0    conda-forge\n",
+      "imageio                   2.16.2                   pypi_0    pypi\n",
+      "imcsegpipe                1.0.0                     dev_0    <develop>\n",
+      "importlib-metadata        4.11.3           py39h6e9494a_1    conda-forge\n",
+      "importlib_resources       5.6.0              pyhd8ed1ab_1    conda-forge\n",
+      "ipykernel                 6.13.0           py39h71a6800_0    conda-forge\n",
+      "ipython                   8.2.0            py39h6e9494a_0    conda-forge\n",
       "ipython_genutils          0.2.0                      py_1    conda-forge\n",
-      "jedi                      0.18.1           py39h6e9494a_0    conda-forge\n",
-      "jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge\n",
+      "jedi                      0.18.1           py39h6e9494a_1    conda-forge\n",
+      "jinja2                    3.1.1              pyhd8ed1ab_0    conda-forge\n",
       "json5                     0.9.5              pyh9f0ad1d_0    conda-forge\n",
       "jsonschema                4.4.0              pyhd8ed1ab_0    conda-forge\n",
-      "jupyter_client            7.1.2              pyhd8ed1ab_0    conda-forge\n",
-      "jupyter_core              4.9.1            py39h6e9494a_1    conda-forge\n",
-      "jupyter_server            1.13.5             pyhd8ed1ab_1    conda-forge\n",
-      "jupyterlab                3.2.9              pyhd8ed1ab_0    conda-forge\n",
-      "jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge\n",
-      "jupyterlab_server         2.10.3             pyhd8ed1ab_0    conda-forge\n",
-      "jupytext                  1.13.6             pyheef035f_0    conda-forge\n",
-      "libcxx                    12.0.1               habf9029_1    conda-forge\n",
+      "jupyter_client            7.2.2              pyhd8ed1ab_1    conda-forge\n",
+      "jupyter_core              4.9.2            py39h6e9494a_0    conda-forge\n",
+      "jupyter_server            1.16.0             pyhd8ed1ab_1    conda-forge\n",
+      "jupyterlab                3.3.3              pyhd8ed1ab_0    conda-forge\n",
+      "jupyterlab_pygments       0.2.0              pyhd8ed1ab_0    conda-forge\n",
+      "jupyterlab_server         2.12.0             pyhd8ed1ab_0    conda-forge\n",
+      "jupytext                  1.13.8             pyh4b9bcc7_0    conda-forge\n",
+      "libcxx                    13.0.1               hc203e6f_0    conda-forge\n",
       "libffi                    3.4.2                h0d85af4_5    conda-forge\n",
       "libsodium                 1.0.18               hbcb3906_1    conda-forge\n",
-      "libzlib                   1.2.11            h9173be1_1013    conda-forge\n",
-      "markdown-it-py            1.1.0              pyhd8ed1ab_0    conda-forge\n",
-      "markupsafe                2.0.1            py39h89e85a6_1    conda-forge\n",
+      "libzlib                   1.2.11            h6c3fc93_1014    conda-forge\n",
+      "markdown-it-py            2.0.1              pyhd8ed1ab_0    conda-forge\n",
+      "markupsafe                2.1.1            py39h63b48b0_1    conda-forge\n",
       "matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge\n",
       "mdit-py-plugins           0.3.0              pyhd8ed1ab_0    conda-forge\n",
+      "mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge\n",
       "mistune                   0.8.4           py39h89e85a6_1005    conda-forge\n",
-      "mypy_extensions           0.4.3            py39h6e9494a_4    conda-forge\n",
-      "nbclassic                 0.3.5              pyhd8ed1ab_0    conda-forge\n",
-      "nbclient                  0.5.10             pyhd8ed1ab_1    conda-forge\n",
-      "nbconvert                 6.4.2            py39h6e9494a_0    conda-forge\n",
-      "nbformat                  5.1.3              pyhd8ed1ab_0    conda-forge\n",
-      "ncurses                   6.3                  he49afe7_0    conda-forge\n",
-      "nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge\n",
-      "notebook                  6.4.8              pyha770c72_0    conda-forge\n",
-      "numpy                     1.22.2                   pypi_0    pypi\n",
-      "openssl                   1.1.1l               h0d85af4_0    conda-forge\n",
+      "nbclassic                 0.3.7              pyhd8ed1ab_0    conda-forge\n",
+      "nbclient                  0.5.13             pyhd8ed1ab_0    conda-forge\n",
+      "nbconvert                 6.5.0              pyhd8ed1ab_0    conda-forge\n",
+      "nbconvert-core            6.5.0              pyhd8ed1ab_0    conda-forge\n",
+      "nbconvert-pandoc          6.5.0              pyhd8ed1ab_0    conda-forge\n",
+      "nbformat                  5.3.0              pyhd8ed1ab_0    conda-forge\n",
+      "ncurses                   6.3                  h96cf925_1    conda-forge\n",
+      "nest-asyncio              1.5.5              pyhd8ed1ab_0    conda-forge\n",
+      "notebook                  6.4.10             pyha770c72_0    conda-forge\n",
+      "notebook-shim             0.1.0              pyhd8ed1ab_0    conda-forge\n",
+      "numpy                     1.22.3                   pypi_0    pypi\n",
+      "openssl                   1.1.1n               h6c3fc93_0    conda-forge\n",
       "packaging                 21.3               pyhd8ed1ab_0    conda-forge\n",
-      "pandas                    1.4.1                    pypi_0    pypi\n",
-      "pandoc                    2.17.1.1             h694c41f_0    conda-forge\n",
+      "pandas                    1.4.2                    pypi_0    pypi\n",
+      "pandoc                    2.18                 h694c41f_0    conda-forge\n",
       "pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge\n",
       "parso                     0.8.3              pyhd8ed1ab_0    conda-forge\n",
-      "pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge\n",
       "pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge\n",
       "pickleshare               0.7.5                   py_1003    conda-forge\n",
-      "pillow                    9.0.1                    pypi_0    pypi\n",
-      "pip                       22.0.3             pyhd8ed1ab_0    conda-forge\n",
-      "platformdirs              2.5.0              pyhd8ed1ab_0    conda-forge\n",
-      "prometheus_client         0.13.1             pyhd8ed1ab_0    conda-forge\n",
-      "prompt-toolkit            3.0.27             pyha770c72_0    conda-forge\n",
+      "pillow                    9.1.0                    pypi_0    pypi\n",
+      "pip                       22.0.4             pyhd8ed1ab_0    conda-forge\n",
+      "prometheus_client         0.14.1             pyhd8ed1ab_0    conda-forge\n",
+      "prompt-toolkit            3.0.29             pyha770c72_0    conda-forge\n",
+      "psutil                    5.9.0            py39h63b48b0_1    conda-forge\n",
       "ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge\n",
       "pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge\n",
       "pycparser                 2.21               pyhd8ed1ab_0    conda-forge\n",
       "pygments                  2.11.2             pyhd8ed1ab_0    conda-forge\n",
       "pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge\n",
-      "pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge\n",
-      "pyrsistent                0.18.1           py39h89e85a6_0    conda-forge\n",
-      "pysocks                   1.7.1            py39h6e9494a_4    conda-forge\n",
-      "python                    3.9.10          h1dd9edd_2_cpython    conda-forge\n",
+      "pyparsing                 3.0.8              pyhd8ed1ab_0    conda-forge\n",
+      "pyrsistent                0.18.1           py39h63b48b0_1    conda-forge\n",
+      "pysocks                   1.7.1            py39h6e9494a_5    conda-forge\n",
+      "python                    3.9.12          h8b4d769_1_cpython    conda-forge\n",
       "python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge\n",
+      "python-fastjsonschema     2.15.3             pyhd8ed1ab_0    conda-forge\n",
       "python_abi                3.9                      2_cp39    conda-forge\n",
-      "pytz                      2021.3             pyhd8ed1ab_0    conda-forge\n",
-      "pyyaml                    6.0              py39h89e85a6_3    conda-forge\n",
-      "pyzmq                     22.3.0           py39h7fec2f1_1    conda-forge\n",
+      "pytz                      2022.1             pyhd8ed1ab_0    conda-forge\n",
+      "pyyaml                    6.0              py39h63b48b0_4    conda-forge\n",
+      "pyzmq                     22.3.0           py39hc2dc7ec_2    conda-forge\n",
       "readimc                   0.6.1                    pypi_0    pypi\n",
       "readline                  8.1                  h05e3726_0    conda-forge\n",
       "requests                  2.27.1             pyhd8ed1ab_0    conda-forge\n",
       "scipy                     1.8.0                    pypi_0    pypi\n",
       "send2trash                1.8.0              pyhd8ed1ab_0    conda-forge\n",
-      "setuptools                60.9.0           py39h6e9494a_0    conda-forge\n",
+      "setuptools                62.1.0           py39h6e9494a_0    conda-forge\n",
       "six                       1.16.0             pyh6c4a22f_0    conda-forge\n",
-      "sniffio                   1.2.0            py39h6e9494a_2    conda-forge\n",
-      "sqlite                    3.37.0               h23a322b_0    conda-forge\n",
-      "stack_data                0.1.4              pyhd8ed1ab_0    conda-forge\n",
-      "terminado                 0.13.1           py39h6e9494a_0    conda-forge\n",
-      "testpath                  0.5.0              pyhd8ed1ab_0    conda-forge\n",
-      "tifffile                  2022.2.9                 pypi_0    pypi\n",
-      "tk                        8.6.11               h5dbffcc_1    conda-forge\n",
+      "sniffio                   1.2.0            py39h6e9494a_3    conda-forge\n",
+      "soupsieve                 2.3.1              pyhd8ed1ab_0    conda-forge\n",
+      "sqlite                    3.38.2               hb516253_0    conda-forge\n",
+      "stack_data                0.2.0              pyhd8ed1ab_0    conda-forge\n",
+      "terminado                 0.13.3           py39h6e9494a_1    conda-forge\n",
+      "tifffile                  2022.4.8                 pypi_0    pypi\n",
+      "tinycss2                  1.1.1              pyhd8ed1ab_0    conda-forge\n",
+      "tk                        8.6.12               h5dbffcc_0    conda-forge\n",
       "toml                      0.10.2             pyhd8ed1ab_0    conda-forge\n",
-      "tomli                     2.0.1              pyhd8ed1ab_0    conda-forge\n",
-      "tornado                   6.1              py39h89e85a6_2    conda-forge\n",
+      "tornado                   6.1              py39h63b48b0_3    conda-forge\n",
       "traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge\n",
-      "typed-ast                 1.5.2            py39h89e85a6_0    conda-forge\n",
-      "typing_extensions         4.0.1              pyha770c72_0    conda-forge\n",
-      "tzdata                    2021e                he74cb21_0    conda-forge\n",
-      "urllib3                   1.26.8             pyhd8ed1ab_1    conda-forge\n",
+      "typing_extensions         4.1.1              pyha770c72_0    conda-forge\n",
+      "tzdata                    2022a                h191b570_0    conda-forge\n",
+      "urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge\n",
       "wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge\n",
       "webencodings              0.5.1                      py_1    conda-forge\n",
-      "websocket-client          1.2.3              pyhd8ed1ab_0    conda-forge\n",
+      "websocket-client          1.3.2              pyhd8ed1ab_0    conda-forge\n",
       "wheel                     0.37.1             pyhd8ed1ab_0    conda-forge\n",
       "xtiff                     0.7.7                    pypi_0    pypi\n",
       "xz                        5.2.5                haf1e3a3_1    conda-forge\n",
       "yaml                      0.2.5                h0d85af4_2    conda-forge\n",
       "zeromq                    4.3.4                he49afe7_1    conda-forge\n",
-      "zipp                      3.7.0              pyhd8ed1ab_1    conda-forge\n",
-      "zlib                      1.2.11            h9173be1_1013    conda-forge\n"
+      "zipp                      3.8.0              pyhd8ed1ab_0    conda-forge\n",
+      "zlib                      1.2.11            h6c3fc93_1014    conda-forge\n"
      ]
     }
    ],
    "source": [
     "!conda list"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "688e2f34-8852-49b1-9c67-5e711414f7bf",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
diff --git a/scripts/imc_preprocessing.py b/scripts/imc_preprocessing.py
index 29218ba..c7bbc11 100644
--- a/scripts/imc_preprocessing.py
+++ b/scripts/imc_preprocessing.py
@@ -250,3 +250,5 @@
 
 # %%
 # !conda list
+
+# %%

From 1605c6f30cbe91bdfeffbd698542794eec129e55 Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Mon, 11 Apr 2022 20:00:31 +0200
Subject: [PATCH 5/6] Updated CHANGELOG

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 65fa7b6..1780c60 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [3.2]
+
+ - sort channels by metal tag when creating the ilastik and full stacks
+
 ## [3.1]
 
  - fixed git submodule issue

From 83a81d14502ca0cb70ae33d80c72aefbd3f64aee Mon Sep 17 00:00:00 2001
From: nilseling <nils.eling@gmx.de>
Date: Mon, 11 Apr 2022 20:07:11 +0200
Subject: [PATCH 6/6] Updated classifier link

---
 scripts/download_examples.ipynb | 2 +-
 scripts/download_examples.py    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/download_examples.ipynb b/scripts/download_examples.ipynb
index 8c0bb3f..95659ec 100644
--- a/scripts/download_examples.ipynb
+++ b/scripts/download_examples.ipynb
@@ -60,7 +60,7 @@
     "# Ilastik project\n",
     "ilastik_project = Path(\"..\") / \"IMCWorkflow.ilp\"\n",
     "if not ilastik_project.exists():\n",
-    "    request.urlretrieve(\"https://zenodo.org/record/6404960/files/IMCWorkflow.ilp\", ilastik_project)\n",
+    "    request.urlretrieve(\"https://zenodo.org/record/6449127/files/IMCWorkflow.ilp\", ilastik_project)\n",
     "    \n",
     "# Sample metadata\n",
     "sample_metadata = Path(\"..\") / \"sample_metadata.xlsx\"\n",
diff --git a/scripts/download_examples.py b/scripts/download_examples.py
index b2f6636..b4bdbf7 100644
--- a/scripts/download_examples.py
+++ b/scripts/download_examples.py
@@ -43,7 +43,7 @@
 # Ilastik project
 ilastik_project = Path("..") / "IMCWorkflow.ilp"
 if not ilastik_project.exists():
-    request.urlretrieve("https://zenodo.org/record/6404960/files/IMCWorkflow.ilp", ilastik_project)
+    request.urlretrieve("https://zenodo.org/record/6449127/files/IMCWorkflow.ilp", ilastik_project)
     
 # Sample metadata
 sample_metadata = Path("..") / "sample_metadata.xlsx"