diff --git a/.gitignore b/.gitignore index de60946..0ad7088 100644 --- a/.gitignore +++ b/.gitignore @@ -3,7 +3,8 @@ /.vscode/ /analysis/ /raw/ -sample_metadata.xlsx +sample_metadata.csv + # Byte-compiled / optimized / DLL files __pycache__/ diff --git a/scripts/download_examples.ipynb b/scripts/download_examples.ipynb index e798567..5690de5 100644 --- a/scripts/download_examples.ipynb +++ b/scripts/download_examples.ipynb @@ -19,7 +19,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 4, "id": "83673a33", "metadata": {}, "outputs": [], @@ -63,14 +63,14 @@ " request.urlretrieve(\"https://zenodo.org/record/6449127/files/IMCWorkflow.ilp\", ilastik_project)\n", " \n", "# Sample metadata\n", - "sample_metadata = Path(\"..\") / \"sample_metadata.xlsx\"\n", + "sample_metadata = Path(\"..\") / \"sample_metadata.csv\"\n", "if not sample_metadata.exists():\n", " request.urlretrieve(\"https://zenodo.org/record/7575859/files/sample_metadata.csv\", sample_metadata)" ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 5, "id": "5cebbf89", "metadata": {}, "outputs": [ @@ -81,63 +81,62 @@ "# packages in environment at /Users/nils/opt/anaconda3/envs/imcsegpipe:\n", "#\n", "# Name Version Build Channel\n", - "aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge\n", - "aiosqlite 0.18.0 pyhd8ed1ab_0 conda-forge\n", "anyio 3.6.2 pyhd8ed1ab_0 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 py39ha30fb19_3 conda-forge\n", "asttokens 2.2.1 pyhd8ed1ab_0 conda-forge\n", - "attrs 22.2.0 pyh71513ae_0 conda-forge\n", + "async-lru 2.0.2 pyhd8ed1ab_0 conda-forge\n", + "attrs 23.1.0 pyh71513ae_1 conda-forge\n", "babel 2.12.1 pyhd8ed1ab_1 conda-forge\n", "backcall 0.2.0 pyh9f0ad1d_0 conda-forge\n", "backports 1.0 pyhd8ed1ab_3 conda-forge\n", "backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge\n", - "beautifulsoup4 4.11.2 pyha770c72_0 conda-forge\n", + "beautifulsoup4 4.12.2 pyha770c72_0 conda-forge\n", "bleach 6.0.0 pyhd8ed1ab_0 conda-forge\n", - "brotlipy 0.7.0 py39ha30fb19_1005 conda-forge\n", + "brotli 1.0.9 hb7f2c08_8 conda-forge\n", + "brotli-bin 1.0.9 hb7f2c08_8 conda-forge\n", "bzip2 1.0.8 h0d85af4_4 conda-forge\n", - "ca-certificates 2022.12.7 h033912b_0 conda-forge\n", - "certifi 2022.12.7 pyhd8ed1ab_0 conda-forge\n", + "ca-certificates 2023.5.7 h8857fd0_0 conda-forge\n", + "certifi 2023.5.7 pyhd8ed1ab_0 conda-forge\n", "cffi 1.15.1 py39h131948b_3 conda-forge\n", - "charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge\n", - "comm 0.1.2 pyhd8ed1ab_0 conda-forge\n", - "cryptography 39.0.2 py39hbeae22c_0 conda-forge\n", - "debugpy 1.6.6 py39h7a8716b_0 conda-forge\n", + "charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge\n", + "comm 0.1.3 pyhd8ed1ab_0 conda-forge\n", + "debugpy 1.6.7 py39h7a8716b_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 1.2.0 pyhd8ed1ab_0 conda-forge\n", - "flit-core 3.8.0 pyhd8ed1ab_0 conda-forge\n", + "flit-core 3.9.0 pyhd8ed1ab_0 conda-forge\n", "idna 3.4 pyhd8ed1ab_0 conda-forge\n", - "imageio 2.26.0 pypi_0 pypi\n", + "imageio 2.30.0 pypi_0 pypi\n", "imcsegpipe 1.0.0 pypi_0 pypi\n", - "importlib-metadata 6.0.0 pyha770c72_0 conda-forge\n", - "importlib_metadata 6.0.0 hd8ed1ab_0 conda-forge\n", + "importlib-metadata 6.6.0 pyha770c72_0 conda-forge\n", + "importlib_metadata 6.6.0 hd8ed1ab_0 conda-forge\n", "importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge\n", - "ipykernel 6.21.2 pyh736e0ef_0 conda-forge\n", - "ipython 8.11.0 pyhd1c38e8_0 conda-forge\n", - "ipython_genutils 0.2.0 py_1 conda-forge\n", + "ipykernel 6.23.1 pyh736e0ef_0 conda-forge\n", + "ipython 8.13.2 pyhd1c38e8_0 conda-forge\n", "jedi 0.18.2 pyhd8ed1ab_0 conda-forge\n", "jinja2 3.1.2 pyhd8ed1ab_1 conda-forge\n", "json5 0.9.5 pyh9f0ad1d_0 conda-forge\n", "jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge\n", - "jupyter_client 8.0.3 pyhd8ed1ab_0 conda-forge\n", - "jupyter_core 5.2.0 py39h6e9494a_0 conda-forge\n", + "jupyter-lsp 2.1.0 pyhd8ed1ab_0 conda-forge\n", + "jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge\n", + "jupyter_core 5.3.0 py39h6e9494a_0 conda-forge\n", "jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge\n", - "jupyter_server 2.4.0 pyhd8ed1ab_0 conda-forge\n", - "jupyter_server_fileid 0.8.0 pyhd8ed1ab_0 conda-forge\n", + "jupyter_server 2.6.0 pyhd8ed1ab_0 conda-forge\n", "jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge\n", - "jupyter_server_ydoc 0.6.1 pyhd8ed1ab_0 conda-forge\n", - "jupyter_ydoc 0.2.2 pyhd8ed1ab_0 conda-forge\n", - "jupyterlab 3.6.1 pyhd8ed1ab_0 conda-forge\n", + "jupyterlab 4.0.0 pyhd8ed1ab_1 conda-forge\n", "jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge\n", - "jupyterlab_server 2.20.0 pyhd8ed1ab_0 conda-forge\n", + "jupyterlab_server 2.22.1 pyhd8ed1ab_0 conda-forge\n", "jupytext 1.14.5 pyhcff175f_0 conda-forge\n", - "libcxx 15.0.7 h71dddab_0 conda-forge\n", + "libbrotlicommon 1.0.9 hb7f2c08_8 conda-forge\n", + "libbrotlidec 1.0.9 hb7f2c08_8 conda-forge\n", + "libbrotlienc 1.0.9 hb7f2c08_8 conda-forge\n", + "libcxx 16.0.4 hd57cbcb_0 conda-forge\n", "libffi 3.4.2 h0d85af4_5 conda-forge\n", "libsodium 1.0.18 hbcb3906_1 conda-forge\n", - "libsqlite 3.40.0 ha978bb4_0 conda-forge\n", + "libsqlite 3.42.0 h58db7d2_0 conda-forge\n", "libzlib 1.2.13 hfd90126_4 conda-forge\n", "markdown-it-py 2.2.0 pyhd8ed1ab_0 conda-forge\n", "markupsafe 2.1.2 py39ha30fb19_0 conda-forge\n", @@ -145,81 +144,77 @@ "mdit-py-plugins 0.3.5 pyhd8ed1ab_0 conda-forge\n", "mdurl 0.1.0 pyhd8ed1ab_0 conda-forge\n", "mistune 2.0.5 pyhd8ed1ab_0 conda-forge\n", - "nbclassic 0.5.3 pyhb4ecaf3_3 conda-forge\n", - "nbclient 0.7.2 pyhd8ed1ab_0 conda-forge\n", - "nbconvert 7.2.9 pyhd8ed1ab_0 conda-forge\n", - "nbconvert-core 7.2.9 pyhd8ed1ab_0 conda-forge\n", - "nbconvert-pandoc 7.2.9 pyhd8ed1ab_0 conda-forge\n", - "nbformat 5.7.3 pyhd8ed1ab_0 conda-forge\n", + "nbclient 0.8.0 pyhd8ed1ab_0 conda-forge\n", + "nbconvert-core 7.4.0 pyhd8ed1ab_0 conda-forge\n", + "nbformat 5.8.0 pyhd8ed1ab_0 conda-forge\n", "ncurses 6.3 h96cf925_1 conda-forge\n", "nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge\n", - "notebook 6.5.3 pyha770c72_0 conda-forge\n", - "notebook-shim 0.2.2 pyhd8ed1ab_0 conda-forge\n", - "numpy 1.24.2 pypi_0 pypi\n", - "openssl 3.0.8 hfd90126_0 conda-forge\n", - "packaging 23.0 pyhd8ed1ab_0 conda-forge\n", - "pandas 1.5.3 pypi_0 pypi\n", - "pandoc 2.19.2 h694c41f_2 conda-forge\n", + "notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge\n", + "numpy 1.24.3 pypi_0 pypi\n", + "openssl 3.1.0 h8a1eda9_3 conda-forge\n", + "overrides 7.3.1 pyhd8ed1ab_0 conda-forge\n", + "packaging 23.1 pyhd8ed1ab_0 conda-forge\n", + "pandas 2.0.2 pypi_0 pypi\n", "pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge\n", "parso 0.8.3 pyhd8ed1ab_0 conda-forge\n", "pexpect 4.8.0 pyh1a96a4e_2 conda-forge\n", "pickleshare 0.7.5 py_1003 conda-forge\n", - "pillow 9.4.0 pypi_0 pypi\n", - "pip 23.0.1 pyhd8ed1ab_0 conda-forge\n", + "pillow 9.5.0 pypi_0 pypi\n", + "pip 23.1.2 pyhd8ed1ab_0 conda-forge\n", "pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge\n", - "platformdirs 3.1.0 pyhd8ed1ab_0 conda-forge\n", - "prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge\n", + "platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge\n", + "prometheus_client 0.17.0 pyhd8ed1ab_0 conda-forge\n", "prompt-toolkit 3.0.38 pyha770c72_0 conda-forge\n", "prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge\n", - "psutil 5.9.4 py39ha30fb19_0 conda-forge\n", + "psutil 5.9.5 py39ha30fb19_0 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 2.14.0 pyhd8ed1ab_0 conda-forge\n", - "pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge\n", + "pygments 2.15.1 pyhd8ed1ab_0 conda-forge\n", + "pyobjc-core 9.1.1 py39h0504f80_0 conda-forge\n", + "pyobjc-framework-cocoa 9.1.1 py39h0504f80_0 conda-forge\n", "pyrsistent 0.19.3 py39ha30fb19_0 conda-forge\n", "pysocks 1.7.1 pyha2e5f31_6 conda-forge\n", "python 3.9.16 h709bd14_0_cpython conda-forge\n", "python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge\n", - "python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge\n", + "python-fastjsonschema 2.17.1 pyhd8ed1ab_0 conda-forge\n", "python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge\n", "python_abi 3.9 3_cp39 conda-forge\n", - "pytz 2022.7.1 pyhd8ed1ab_0 conda-forge\n", + "pytz 2023.3 pyhd8ed1ab_0 conda-forge\n", "pyyaml 6.0 py39ha30fb19_5 conda-forge\n", - "pyzmq 25.0.0 py39hed8f129_0 conda-forge\n", + "pyzmq 25.0.2 py39hed8f129_0 conda-forge\n", "readimc 0.6.2 pypi_0 pypi\n", - "readline 8.1.2 h3899abd_0 conda-forge\n", - "requests 2.28.2 pyhd8ed1ab_0 conda-forge\n", + "readline 8.2 h9e318b2_1 conda-forge\n", + "requests 2.31.0 pyhd8ed1ab_0 conda-forge\n", "rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge\n", "rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge\n", "scipy 1.10.1 pypi_0 pypi\n", - "send2trash 1.8.0 pyhd8ed1ab_0 conda-forge\n", - "setuptools 67.5.1 pyhd8ed1ab_0 conda-forge\n", + "send2trash 1.8.2 pyhd1c38e8_0 conda-forge\n", + "setuptools 67.7.2 pyhd8ed1ab_0 conda-forge\n", "six 1.16.0 pyh6c4a22f_0 conda-forge\n", "sniffio 1.3.0 pyhd8ed1ab_0 conda-forge\n", "soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge\n", "stack_data 0.6.2 pyhd8ed1ab_0 conda-forge\n", "terminado 0.17.1 pyhd1c38e8_0 conda-forge\n", - "tifffile 2023.2.28 pypi_0 pypi\n", + "tifffile 2023.4.12 pypi_0 pypi\n", "tinycss2 1.2.1 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 6.2 py39ha30fb19_1 conda-forge\n", + "tornado 6.3.2 py39hdc70f33_0 conda-forge\n", "traitlets 5.9.0 pyhd8ed1ab_0 conda-forge\n", - "typing-extensions 4.4.0 hd8ed1ab_0 conda-forge\n", - "typing_extensions 4.4.0 pyha770c72_0 conda-forge\n", - "tzdata 2022g h191b570_0 conda-forge\n", - "urllib3 1.26.14 pyhd8ed1ab_0 conda-forge\n", + "typing-extensions 4.6.2 hd8ed1ab_0 conda-forge\n", + "typing_extensions 4.6.2 pyha770c72_0 conda-forge\n", + "typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge\n", + "tzdata 2023.3 pypi_0 pypi\n", + "urllib3 2.0.2 pyhd8ed1ab_0 conda-forge\n", "wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge\n", "webencodings 0.5.1 py_1 conda-forge\n", - "websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge\n", - "wheel 0.38.4 pyhd8ed1ab_0 conda-forge\n", + "websocket-client 1.5.2 pyhd8ed1ab_0 conda-forge\n", + "wheel 0.40.0 pyhd8ed1ab_0 conda-forge\n", "xtiff 0.7.9 pypi_0 pypi\n", "xz 5.2.6 h775f41a_0 conda-forge\n", - "y-py 0.5.9 py39hd4bc93a_0 conda-forge\n", "yaml 0.2.5 h0d85af4_2 conda-forge\n", - "ypy-websocket 0.8.2 pyhd8ed1ab_0 conda-forge\n", "zeromq 4.3.4 he49afe7_1 conda-forge\n", "zipp 3.15.0 pyhd8ed1ab_0 conda-forge\n" ] diff --git a/scripts/download_examples.py b/scripts/download_examples.py index 83b96a6..8208fea 100644 --- a/scripts/download_examples.py +++ b/scripts/download_examples.py @@ -46,7 +46,7 @@ request.urlretrieve("https://zenodo.org/record/6449127/files/IMCWorkflow.ilp", ilastik_project) # Sample metadata -sample_metadata = Path("..") / "sample_metadata.xlsx" +sample_metadata = Path("..") / "sample_metadata.csv" if not sample_metadata.exists(): request.urlretrieve("https://zenodo.org/record/7575859/files/sample_metadata.csv", sample_metadata) diff --git a/scripts/imc_preprocessing.ipynb b/scripts/imc_preprocessing.ipynb index d424bca..8ceea3d 100755 --- a/scripts/imc_preprocessing.ipynb +++ b/scripts/imc_preprocessing.ipynb @@ -80,7 +80,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 2, "id": "59626637", "metadata": { "tags": [] @@ -127,7 +127,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 3, "id": "281ad642", "metadata": { "tags": [] @@ -163,7 +163,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 4, "id": "0ac63953", "metadata": { "tags": [] @@ -197,7 +197,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 5, "id": "1169391e", "metadata": { "tags": [] @@ -247,7 +247,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 6, "id": "ce4a4040", "metadata": { "tags": [] @@ -259,7 +259,7 @@ "PosixPath('../analysis/cpout/panel.csv')" ] }, - "execution_count": 8, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } @@ -281,7 +281,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 7, "id": "0dc3d319", "metadata": { "tags": [] @@ -321,7 +321,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 8, "id": "320202b6", "metadata": { "tags": [] @@ -366,7 +366,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 9, "id": "ece67368", "metadata": { "tags": [] @@ -378,7 +378,7 @@ "PosixPath('../analysis/cpinp/full_channelmeta.csv')" ] }, - "execution_count": 11, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } @@ -398,7 +398,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 10, "id": "d7a25f2b", "metadata": { "tags": [] @@ -444,7 +444,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 11, "id": "e6cb34d5", "metadata": { "tags": [] @@ -457,63 +457,62 @@ "# packages in environment at /Users/nils/opt/anaconda3/envs/imcsegpipe:\n", "#\n", "# Name Version Build Channel\n", - "aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge\n", - "aiosqlite 0.18.0 pyhd8ed1ab_0 conda-forge\n", "anyio 3.6.2 pyhd8ed1ab_0 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 py39ha30fb19_3 conda-forge\n", "asttokens 2.2.1 pyhd8ed1ab_0 conda-forge\n", - "attrs 22.2.0 pyh71513ae_0 conda-forge\n", + "async-lru 2.0.2 pyhd8ed1ab_0 conda-forge\n", + "attrs 23.1.0 pyh71513ae_1 conda-forge\n", "babel 2.12.1 pyhd8ed1ab_1 conda-forge\n", "backcall 0.2.0 pyh9f0ad1d_0 conda-forge\n", "backports 1.0 pyhd8ed1ab_3 conda-forge\n", "backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge\n", - "beautifulsoup4 4.11.2 pyha770c72_0 conda-forge\n", + "beautifulsoup4 4.12.2 pyha770c72_0 conda-forge\n", "bleach 6.0.0 pyhd8ed1ab_0 conda-forge\n", - "brotlipy 0.7.0 py39ha30fb19_1005 conda-forge\n", + "brotli 1.0.9 hb7f2c08_8 conda-forge\n", + "brotli-bin 1.0.9 hb7f2c08_8 conda-forge\n", "bzip2 1.0.8 h0d85af4_4 conda-forge\n", - "ca-certificates 2022.12.7 h033912b_0 conda-forge\n", - "certifi 2022.12.7 pyhd8ed1ab_0 conda-forge\n", + "ca-certificates 2023.5.7 h8857fd0_0 conda-forge\n", + "certifi 2023.5.7 pyhd8ed1ab_0 conda-forge\n", "cffi 1.15.1 py39h131948b_3 conda-forge\n", - "charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge\n", - "comm 0.1.2 pyhd8ed1ab_0 conda-forge\n", - "cryptography 39.0.2 py39hbeae22c_0 conda-forge\n", - "debugpy 1.6.6 py39h7a8716b_0 conda-forge\n", + "charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge\n", + "comm 0.1.3 pyhd8ed1ab_0 conda-forge\n", + "debugpy 1.6.7 py39h7a8716b_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 1.2.0 pyhd8ed1ab_0 conda-forge\n", - "flit-core 3.8.0 pyhd8ed1ab_0 conda-forge\n", + "flit-core 3.9.0 pyhd8ed1ab_0 conda-forge\n", "idna 3.4 pyhd8ed1ab_0 conda-forge\n", - "imageio 2.26.0 pypi_0 pypi\n", + "imageio 2.30.0 pypi_0 pypi\n", "imcsegpipe 1.0.0 pypi_0 pypi\n", - "importlib-metadata 6.0.0 pyha770c72_0 conda-forge\n", - "importlib_metadata 6.0.0 hd8ed1ab_0 conda-forge\n", + "importlib-metadata 6.6.0 pyha770c72_0 conda-forge\n", + "importlib_metadata 6.6.0 hd8ed1ab_0 conda-forge\n", "importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge\n", - "ipykernel 6.21.2 pyh736e0ef_0 conda-forge\n", - "ipython 8.11.0 pyhd1c38e8_0 conda-forge\n", - "ipython_genutils 0.2.0 py_1 conda-forge\n", + "ipykernel 6.23.1 pyh736e0ef_0 conda-forge\n", + "ipython 8.13.2 pyhd1c38e8_0 conda-forge\n", "jedi 0.18.2 pyhd8ed1ab_0 conda-forge\n", "jinja2 3.1.2 pyhd8ed1ab_1 conda-forge\n", "json5 0.9.5 pyh9f0ad1d_0 conda-forge\n", "jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge\n", - "jupyter_client 8.0.3 pyhd8ed1ab_0 conda-forge\n", - "jupyter_core 5.2.0 py39h6e9494a_0 conda-forge\n", + "jupyter-lsp 2.1.0 pyhd8ed1ab_0 conda-forge\n", + "jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge\n", + "jupyter_core 5.3.0 py39h6e9494a_0 conda-forge\n", "jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge\n", - "jupyter_server 2.4.0 pyhd8ed1ab_0 conda-forge\n", - "jupyter_server_fileid 0.8.0 pyhd8ed1ab_0 conda-forge\n", + "jupyter_server 2.6.0 pyhd8ed1ab_0 conda-forge\n", "jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge\n", - "jupyter_server_ydoc 0.6.1 pyhd8ed1ab_0 conda-forge\n", - "jupyter_ydoc 0.2.2 pyhd8ed1ab_0 conda-forge\n", - "jupyterlab 3.6.1 pyhd8ed1ab_0 conda-forge\n", + "jupyterlab 4.0.0 pyhd8ed1ab_1 conda-forge\n", "jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge\n", - "jupyterlab_server 2.20.0 pyhd8ed1ab_0 conda-forge\n", + "jupyterlab_server 2.22.1 pyhd8ed1ab_0 conda-forge\n", "jupytext 1.14.5 pyhcff175f_0 conda-forge\n", - "libcxx 15.0.7 h71dddab_0 conda-forge\n", + "libbrotlicommon 1.0.9 hb7f2c08_8 conda-forge\n", + "libbrotlidec 1.0.9 hb7f2c08_8 conda-forge\n", + "libbrotlienc 1.0.9 hb7f2c08_8 conda-forge\n", + "libcxx 16.0.4 hd57cbcb_0 conda-forge\n", "libffi 3.4.2 h0d85af4_5 conda-forge\n", "libsodium 1.0.18 hbcb3906_1 conda-forge\n", - "libsqlite 3.40.0 ha978bb4_0 conda-forge\n", + "libsqlite 3.42.0 h58db7d2_0 conda-forge\n", "libzlib 1.2.13 hfd90126_4 conda-forge\n", "markdown-it-py 2.2.0 pyhd8ed1ab_0 conda-forge\n", "markupsafe 2.1.2 py39ha30fb19_0 conda-forge\n", @@ -521,81 +520,77 @@ "mdit-py-plugins 0.3.5 pyhd8ed1ab_0 conda-forge\n", "mdurl 0.1.0 pyhd8ed1ab_0 conda-forge\n", "mistune 2.0.5 pyhd8ed1ab_0 conda-forge\n", - "nbclassic 0.5.3 pyhb4ecaf3_3 conda-forge\n", - "nbclient 0.7.2 pyhd8ed1ab_0 conda-forge\n", - "nbconvert 7.2.9 pyhd8ed1ab_0 conda-forge\n", - "nbconvert-core 7.2.9 pyhd8ed1ab_0 conda-forge\n", - "nbconvert-pandoc 7.2.9 pyhd8ed1ab_0 conda-forge\n", - "nbformat 5.7.3 pyhd8ed1ab_0 conda-forge\n", + "nbclient 0.8.0 pyhd8ed1ab_0 conda-forge\n", + "nbconvert-core 7.4.0 pyhd8ed1ab_0 conda-forge\n", + "nbformat 5.8.0 pyhd8ed1ab_0 conda-forge\n", "ncurses 6.3 h96cf925_1 conda-forge\n", "nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge\n", - "notebook 6.5.3 pyha770c72_0 conda-forge\n", - "notebook-shim 0.2.2 pyhd8ed1ab_0 conda-forge\n", - "numpy 1.24.2 pypi_0 pypi\n", - "openssl 3.0.8 hfd90126_0 conda-forge\n", - "packaging 23.0 pyhd8ed1ab_0 conda-forge\n", - "pandas 1.5.3 pypi_0 pypi\n", - "pandoc 2.19.2 h694c41f_2 conda-forge\n", + "notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge\n", + "numpy 1.24.3 pypi_0 pypi\n", + "openssl 3.1.0 h8a1eda9_3 conda-forge\n", + "overrides 7.3.1 pyhd8ed1ab_0 conda-forge\n", + "packaging 23.1 pyhd8ed1ab_0 conda-forge\n", + "pandas 2.0.2 pypi_0 pypi\n", "pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge\n", "parso 0.8.3 pyhd8ed1ab_0 conda-forge\n", "pexpect 4.8.0 pyh1a96a4e_2 conda-forge\n", "pickleshare 0.7.5 py_1003 conda-forge\n", - "pillow 9.4.0 pypi_0 pypi\n", - "pip 23.0.1 pyhd8ed1ab_0 conda-forge\n", + "pillow 9.5.0 pypi_0 pypi\n", + "pip 23.1.2 pyhd8ed1ab_0 conda-forge\n", "pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge\n", - "platformdirs 3.1.0 pyhd8ed1ab_0 conda-forge\n", - "prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge\n", + "platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge\n", + "prometheus_client 0.17.0 pyhd8ed1ab_0 conda-forge\n", "prompt-toolkit 3.0.38 pyha770c72_0 conda-forge\n", "prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge\n", - "psutil 5.9.4 py39ha30fb19_0 conda-forge\n", + "psutil 5.9.5 py39ha30fb19_0 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 2.14.0 pyhd8ed1ab_0 conda-forge\n", - "pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge\n", + "pygments 2.15.1 pyhd8ed1ab_0 conda-forge\n", + "pyobjc-core 9.1.1 py39h0504f80_0 conda-forge\n", + "pyobjc-framework-cocoa 9.1.1 py39h0504f80_0 conda-forge\n", "pyrsistent 0.19.3 py39ha30fb19_0 conda-forge\n", "pysocks 1.7.1 pyha2e5f31_6 conda-forge\n", "python 3.9.16 h709bd14_0_cpython conda-forge\n", "python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge\n", - "python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge\n", + "python-fastjsonschema 2.17.1 pyhd8ed1ab_0 conda-forge\n", "python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge\n", "python_abi 3.9 3_cp39 conda-forge\n", - "pytz 2022.7.1 pyhd8ed1ab_0 conda-forge\n", + "pytz 2023.3 pyhd8ed1ab_0 conda-forge\n", "pyyaml 6.0 py39ha30fb19_5 conda-forge\n", - "pyzmq 25.0.0 py39hed8f129_0 conda-forge\n", + "pyzmq 25.0.2 py39hed8f129_0 conda-forge\n", "readimc 0.6.2 pypi_0 pypi\n", - "readline 8.1.2 h3899abd_0 conda-forge\n", - "requests 2.28.2 pyhd8ed1ab_0 conda-forge\n", + "readline 8.2 h9e318b2_1 conda-forge\n", + "requests 2.31.0 pyhd8ed1ab_0 conda-forge\n", "rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge\n", "rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge\n", "scipy 1.10.1 pypi_0 pypi\n", - "send2trash 1.8.0 pyhd8ed1ab_0 conda-forge\n", - "setuptools 67.5.1 pyhd8ed1ab_0 conda-forge\n", + "send2trash 1.8.2 pyhd1c38e8_0 conda-forge\n", + "setuptools 67.7.2 pyhd8ed1ab_0 conda-forge\n", "six 1.16.0 pyh6c4a22f_0 conda-forge\n", "sniffio 1.3.0 pyhd8ed1ab_0 conda-forge\n", "soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge\n", "stack_data 0.6.2 pyhd8ed1ab_0 conda-forge\n", "terminado 0.17.1 pyhd1c38e8_0 conda-forge\n", - "tifffile 2023.2.28 pypi_0 pypi\n", + "tifffile 2023.4.12 pypi_0 pypi\n", "tinycss2 1.2.1 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 6.2 py39ha30fb19_1 conda-forge\n", + "tornado 6.3.2 py39hdc70f33_0 conda-forge\n", "traitlets 5.9.0 pyhd8ed1ab_0 conda-forge\n", - "typing-extensions 4.4.0 hd8ed1ab_0 conda-forge\n", - "typing_extensions 4.4.0 pyha770c72_0 conda-forge\n", - "tzdata 2022g h191b570_0 conda-forge\n", - "urllib3 1.26.14 pyhd8ed1ab_0 conda-forge\n", + "typing-extensions 4.6.2 hd8ed1ab_0 conda-forge\n", + "typing_extensions 4.6.2 pyha770c72_0 conda-forge\n", + "typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge\n", + "tzdata 2023.3 pypi_0 pypi\n", + "urllib3 2.0.2 pyhd8ed1ab_0 conda-forge\n", "wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge\n", "webencodings 0.5.1 py_1 conda-forge\n", - "websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge\n", - "wheel 0.38.4 pyhd8ed1ab_0 conda-forge\n", + "websocket-client 1.5.2 pyhd8ed1ab_0 conda-forge\n", + "wheel 0.40.0 pyhd8ed1ab_0 conda-forge\n", "xtiff 0.7.9 pypi_0 pypi\n", "xz 5.2.6 h775f41a_0 conda-forge\n", - "y-py 0.5.9 py39hd4bc93a_0 conda-forge\n", "yaml 0.2.5 h0d85af4_2 conda-forge\n", - "ypy-websocket 0.8.2 pyhd8ed1ab_0 conda-forge\n", "zeromq 4.3.4 he49afe7_1 conda-forge\n", "zipp 3.15.0 pyhd8ed1ab_0 conda-forge\n" ]