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GitHub / maxime915 / msi_zarr_analysis

Analysis tools for Mass Spectrometry Images encoded as OME Zarr (see pims-plugin-format-msi)

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxime915%2Fmsi_zarr_analysis

Stars: 0
Forks: 0
Open Issues: 0

License: apache-2.0
Language: Jupyter Notebook
Repo Size: 30.1 MB
Dependencies: 263

Created: about 2 years ago
Updated: 9 months ago
Last pushed: over 1 year ago
Last synced: 9 months ago

Files

Readme

Dependencies

environment.yml pypi

tensorstore *

requirements.txt pypi

affine =2.3.1=pyhd8ed1ab_0
alsa-lib =1.2.6.1=h7f98852_0
aom =3.5.0=h27087fc_0
asciitree =0.3.3=py_2
asttokens =2.0.8=pyhd8ed1ab_0
attr =2.5.1=h166bdaf_1
attrs =22.1.0=pyh71513ae_1
backcall =0.2.0=pyh9f0ad1d_0
backports =1.0=py_2
backports.functools_lru_cache =1.6.4=pyhd8ed1ab_0
blosc =1.21.1=h83bc5f7_3
boost-cpp =1.78.0=h75c5d50_1
brotli =1.0.9=h166bdaf_8
brotli-bin =1.0.9=h166bdaf_8
brunsli =0.1=h9c3ff4c_0
bzip2 =1.0.8=h7f98852_4
c-ares =1.18.1=h7f98852_0
c-blosc2 =2.4.3=h7a311fb_0
ca-certificates =2022.9.24=ha878542_0
cachecontrol =0.12.11=pypi_0
cairo =1.16.0=ha61ee94_1014
certifi =2022.9.24=pyhd8ed1ab_0
cfitsio =4.1.0=hd9d235c_0
charls =2.3.4=h9c3ff4c_0
charset-normalizer =2.1.1=pypi_0
click =8.1.3=unix_pyhd8ed1ab_2
click-plugins =1.1.1=py_0
cligj =0.7.2=pyhd8ed1ab_1
cloudpickle =2.2.0=pyhd8ed1ab_0
colorama =0.4.6=pyhd8ed1ab_0
contourpy =1.0.5=py310hbf28c38_1
curl =7.86.0=h7bff187_0
cycler =0.11.0=pyhd8ed1ab_0
cytomine-python-client =2.8.3=dev_0
cytoolz =0.12.0=py310h5764c6d_1
daal4py =2021.5.0=py310hb6ee220_0
dal =2021.5.1=ha770c72_803
dask-core =2022.10.1=pyhd8ed1ab_0
dav1d =1.0.0=h166bdaf_1
dbus =1.13.6=h5008d03_3
decorator =5.1.1=pyhd8ed1ab_0
entrypoints =0.4=pyhd8ed1ab_0
exceptiongroup =1.0.0=pyhd8ed1ab_0
executing =1.1.1=pyhd8ed1ab_0
expat =2.5.0=h27087fc_0
fasteners =0.17.3=pyhd8ed1ab_0
fftw =3.3.10=nompi_hf0379b8_105
font-ttf-dejavu-sans-mono =2.37=hab24e00_0
font-ttf-inconsolata =3.000=h77eed37_0
font-ttf-source-code-pro =2.038=h77eed37_0
font-ttf-ubuntu =0.83=hab24e00_0
fontconfig =2.14.1=hc2a2eb6_0
fonts-conda-ecosystem =1=0
fonts-conda-forge =1=0
fonttools =4.38.0=py310h5764c6d_1
freetype =2.12.1=hca18f0e_0
freexl =1.0.6=h166bdaf_1
fsspec =2022.10.0=pyhd8ed1ab_0
future =0.18.2=pyhd8ed1ab_6
geos =3.11.0=h27087fc_0
geotiff =1.7.1=ha76d385_4
gettext =0.21.1=h27087fc_0
giflib =5.2.1=h36c2ea0_2
glib =2.74.1=h6239696_0
glib-tools =2.74.1=h6239696_0
gst-plugins-base =1.20.3=hf6a322e_0
gstreamer =1.20.3=hd4edc92_2
hdf4 =4.2.15=h9772cbc_5
hdf5 =1.12.2=nompi_h2386368_100
icu =70.1=h27087fc_0
idna =3.4=pypi_0
imagecodecs =2022.9.26=py310h90cd304_3
imageio =2.22.0=pyhfa7a67d_0
iniconfig =1.1.1=pyh9f0ad1d_0
ipython =8.6.0=pyh41d4057_1
jack =0.125.0=hf484d3e_1001
jedi =0.18.1=pyhd8ed1ab_2
joblib =1.2.0=pyhd8ed1ab_0
jpeg =9e=h166bdaf_2
json-c =0.16=hc379101_0
jxrlib =1.1=h7f98852_2
kealib =1.4.15=ha7026e8_1
keyutils =1.6.1=h166bdaf_0
kiwisolver =1.4.4=py310hbf28c38_1
krb5 =1.19.3=h3790be6_0
lcms2 =2.13.1=h6ed2654_0
ld_impl_linux-64 =2.39=hc81fddc_0
lerc =4.0.0=h27087fc_0
libaec =1.0.6=h9c3ff4c_0
libavif =0.11.1=h5cdd6b5_0
libblas =3.9.0=16_linux64_openblas
libbrotlicommon =1.0.9=h166bdaf_8
libbrotlidec =1.0.9=h166bdaf_8
libbrotlienc =1.0.9=h166bdaf_8
libcap =2.64=ha37c62d_0
libcblas =3.9.0=16_linux64_openblas
libclang =14.0.6=default_h2e3cab8_0
libclang13 =14.0.6=default_h3a83d3e_0
libcups =2.3.3=h3e49a29_2
libcurl =7.86.0=h7bff187_0
libdap4 =3.20.6=hd7c4107_2
libdb =6.1.26=0
libdeflate =1.14=h166bdaf_0
libedit =3.1.20191231=he28a2e2_2
libev =4.33=h516909a_1
libevent =2.1.10=h9b69904_4
libffi =3.4.2=h7f98852_5
libflac =1.3.4=h27087fc_0
libgcc =7.2.0=h69d50b8_2
libgcc-ng =12.2.0=h65d4601_19
libgdal =3.5.2=hf663712_5
libgfortran-ng =12.2.0=h69a702a_19
libgfortran5 =12.2.0=h337968e_19
libglib =2.74.1=h7a41b64_0
libgomp =12.2.0=h65d4601_19
libiconv =1.17=h166bdaf_0
libkml =1.3.0=h37653c0_1015
liblapack =3.9.0=16_linux64_openblas
libllvm11 =11.1.0=he0ac6c6_5
libllvm14 =14.0.6=he0ac6c6_0
libnetcdf =4.8.1=nompi_h261ec11_105
libnghttp2 =1.47.0=hdcd2b5c_1
libnsl =2.0.0=h7f98852_0
libogg =1.3.4=h7f98852_1
libopenblas =0.3.21=pthreads_h78a6416_3
libopus =1.3.1=h7f98852_1
libpng =1.6.38=h753d276_0
libpq =14.5=hd77ab85_1
librttopo =1.1.0=hf730bdb_11
libsndfile =1.0.31=h9c3ff4c_1
libspatialite =5.0.1=hfbd986c_21
libsqlite =3.39.4=h753d276_0
libssh2 =1.10.0=haa6b8db_3
libstdcxx-ng =12.2.0=h46fd767_19
libtiff =4.4.0=h55922b4_4
libtool =2.4.6=h9c3ff4c_1008
libuuid =2.32.1=h7f98852_1000
libvorbis =1.3.7=h9c3ff4c_0
libwebp-base =1.2.4=h166bdaf_0
libxcb =1.13=h7f98852_1004
libxkbcommon =1.0.3=he3ba5ed_0
libxml2 =2.10.3=h7463322_0
libzip =1.9.2=hc869a4a_1
libzlib =1.2.13=h166bdaf_4
libzopfli =1.0.3=h9c3ff4c_0
llvmlite =0.39.1=py310h58363a5_1
locket =1.0.0=pyhd8ed1ab_0
lz4-c =1.9.3=h9c3ff4c_1
matplotlib =3.6.1=py310hff52083_1
matplotlib-base =3.6.1=py310h8d5ebf3_1
matplotlib-inline =0.1.6=pyhd8ed1ab_0
mpi =1.0=mpich
mpich =4.0.2=h846660c_100
msgpack-python =1.0.4=py310hbf28c38_1
munkres =1.0.7=py_1
mysql-common =8.0.31=haf5c9bc_0
mysql-libs =8.0.31=h28c427c_0
ncurses =6.3=h27087fc_1
networkx =2.8.7=pyhd8ed1ab_0
nspr =4.32=h9c3ff4c_1
nss =3.78=h2350873_0
numba =0.56.3=py310ha5257ce_0
numcodecs =0.10.2=py310hd8f1fbe_0
numpy =1.23.4=py310h53a5b5f_1
opencv-python-headless =4.6.0.66=pypi_0
openjpeg =2.5.0=h7d73246_1
openssl =1.1.1q=h166bdaf_1
packaging =21.3=pyhd8ed1ab_0
pandas =1.5.1=py310h769672d_1
parso =0.8.3=pyhd8ed1ab_0
partd =1.3.0=pyhd8ed1ab_0
pcre =8.45=h9c3ff4c_0
pcre2 =10.37=hc3806b6_1
pexpect =4.8.0=pyh9f0ad1d_2
pickleshare =0.7.5=py_1003
pillow =9.2.0=py310h454ad03_3
pip =22.3=pyhd8ed1ab_0
pixman =0.40.0=h36c2ea0_0
pluggy =1.0.0=pyhd8ed1ab_5
ply =3.11=py_1
poppler =22.10.0=h92391eb_0
poppler-data =0.4.11=hd8ed1ab_0
postgresql =14.5=hdeef612_1
proj =9.1.0=h93bde94_0
prompt-toolkit =3.0.31=pyha770c72_0
pthread-stubs =0.4=h36c2ea0_1001
ptyprocess =0.7.0=pyhd3deb0d_0
pulseaudio =14.0=h583eb01_5
pure_eval =0.2.2=pyhd8ed1ab_0
pygments =2.13.0=pyhd8ed1ab_0
pyimzml =1.5.1=pyh5e36f6f_0
pyparsing =3.0.9=pyhd8ed1ab_0
pyqt =5.15.7=py310h29803b5_0
pyqt5-sip =12.11.0=py310hd8f1fbe_0
pytest =7.2.0=pyhd8ed1ab_2
python =3.10.6=h582c2e5_0_cpython
python-dateutil =2.8.2=pyhd8ed1ab_0
python_abi =3.10=2_cp310
pytz =2022.5=pyhd8ed1ab_0
pywavelets =1.3.0=py310hde88566_2
pyyaml =6.0=py310h5764c6d_5
qt-main =5.15.4=ha5833f6_2
rasterio =1.3.3=py310hb8c21e3_1
readline =8.1.2=h0f457ee_0
requests =2.28.1=pypi_0
requests-toolbelt =0.10.1=pypi_0
scikit-image =0.19.3=py310h769672d_2
scikit-learn =1.1.3=py310h0c3af53_1
scikit-learn-intelex =2021.5.0=py310hff52083_1
scipy =1.9.3=py310hdfbd76f_1
setuptools =65.5.0=pyhd8ed1ab_0
shapely =1.8.5.post1=pypi_0
sip =6.6.2=py310hd8f1fbe_0
six =1.16.0=pyh6c4a22f_0
snappy =1.1.9=hbd366e4_1
snuggs =1.4.7=py_0
sqlite =3.39.4=h4ff8645_0
stack_data =0.5.1=pyhd8ed1ab_0
tbb =2021.6.0=h924138e_1
tensorstore =0.1.27=pypi_0
threadpoolctl =3.1.0=pyh8a188c0_0
tifffile =2022.10.10=pyhd8ed1ab_0
tiledb =2.11.3=h1e4a385_1
tk =8.6.12=h27826a3_0
toml =0.10.2=pyhd8ed1ab_0
tomli =2.0.1=pyhd8ed1ab_0
toolz =0.12.0=pyhd8ed1ab_0
tornado =6.2=py310h5764c6d_1
traitlets =5.5.0=pyhd8ed1ab_0
typing-extensions =4.4.0=hd8ed1ab_0
typing_extensions =4.4.0=pyha770c72_0
tzcode =2022e=h166bdaf_0
tzdata =2022e=h191b570_0
unicodedata2 =14.0.0=py310h5764c6d_2
urllib3 =1.26.12=pypi_0
wcwidth =0.2.5=pyh9f0ad1d_2
wheel =0.37.1=pyhd8ed1ab_0
wheezy.template =0.1.178=pyh864c0ab_0
xcb-util =0.4.0=h166bdaf_0
xcb-util-image =0.4.0=h166bdaf_0
xcb-util-keysyms =0.4.0=h166bdaf_0
xcb-util-renderutil =0.3.9=h166bdaf_0
xcb-util-wm =0.4.1=h166bdaf_0
xerces-c =3.2.4=h55805fa_1
xorg-kbproto =1.0.7=h7f98852_1002
xorg-libice =1.0.10=h7f98852_0
xorg-libsm =1.2.3=hd9c2040_1000
xorg-libx11 =1.7.2=h7f98852_0
xorg-libxau =1.0.9=h7f98852_0
xorg-libxdmcp =1.1.3=h7f98852_0
xorg-libxext =1.3.4=h7f98852_1
xorg-libxrender =0.9.10=h7f98852_1003
xorg-renderproto =0.11.1=h7f98852_1002
xorg-xextproto =7.3.0=h7f98852_1002
xorg-xproto =7.0.31=h7f98852_1007
xz =5.2.6=h166bdaf_0
yaml =0.2.5=h7f98852_2
zarr =2.13.3=pyhd8ed1ab_0
zfp =1.0.0=h27087fc_3
zlib =1.2.13=h166bdaf_4
zlib-ng =2.0.6=h166bdaf_0
zstd =1.5.2=h6239696_4