Dependencies for full pipeline

[smith6jt-cop]

Hello,

I successfully generated a config.json file and many dependencies were installed. However, after

python run_pipeline.py ./config.json

I find that numpy and frozendict are not in my environment created with requirements.txt as instructed. I installed these manually, but now I get:

Traceback (most recent call last):
File "run_pipeline.py", line 2, in
from pipeline import pipeline
File "/home/smith6jt/CellSegmentationEvaluator/full_pipeline/pipeline/pipeline.py", line 9, in
from .segmentation.run_segmentation import *
File "/home/smith6jt/CellSegmentationEvaluator/full_pipeline/pipeline/segmentation/run_segmentation.py", line 4, in
from .input_channels import get_input_channels
File "/home/smith6jt/CellSegmentationEvaluator/full_pipeline/pipeline/segmentation/input_channels.py", line 3, in
from skimage.external.tifffile import TiffFile
ModuleNotFoundError: No module named 'skimage.external'

Before going any further, please let me know if I likely made a mistake or if there needs to be an update to the requirements list. I am in the same conda environment I used for generating the quality score, Windows Ubuntu 22.04.3 LTS (GNU/Linux 5.15.133.1-microsoft-standard-WSL2 x86_64)

Here is the result from my conda list

Name Version Build Channel

_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
aicsimageio 4.9.4 pypi_0 pypi
annotated-types 0.6.0 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
beautifulsoup4 4.12.2 pypi_0 pypi
bfio 2.3.3 pypi_0 pypi
bioformats-jar 2020.5.27 pypi_0 pypi
blas 1.0 mkl
ca-certificates 2023.11.17 hbcca054_0 conda-forge
certifi 2023.11.17 pypi_0 pypi
charset-normalizer 3.3.2 pypi_0 pypi
click 8.1.7 pypi_0 pypi
cloudpickle 3.0.0 pypi_0 pypi
contourpy 1.1.1 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
dask 2023.5.0 pypi_0 pypi
elementpath 4.1.5 pypi_0 pypi
fasteners 0.19 pypi_0 pypi
filelock 3.13.1 pypi_0 pypi
fonttools 4.46.0 pypi_0 pypi
frozendict 2.3.0 pypi_0 pypi
fsspec 2023.12.1 pypi_0 pypi
gdown 4.7.1 pypi_0 pypi
idna 3.6 pypi_0 pypi
imagecodecs 2023.3.16 pypi_0 pypi
imageio 2.33.0 pypi_0 pypi
importlib-metadata 7.0.0 pypi_0 pypi
importlib-resources 6.1.1 pypi_0 pypi
importlib_metadata 6.0.0 hd3eb1b0_0
intel-openmp 2021.4.0 h06a4308_3561
jgo 1.0.5 pypi_0 pypi
joblib 1.3.2 pypi_0 pypi
jpype1 1.4.1 pypi_0 pypi
kiwisolver 1.4.5 pypi_0 pypi
lazy-loader 0.3 pypi_0 pypi
libedit 3.1.20221030 h5eee18b_0
libffi 3.2.1 hf484d3e_1007
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libllvm11 11.1.0 h9e868ea_6
libstdcxx-ng 11.2.0 h1234567_1
llvmlite 0.39.1 py38he621ea3_0
locket 1.0.0 pypi_0 pypi
lxml 4.9.3 pypi_0 pypi
matplotlib 3.7.4 pypi_0 pypi
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py38h7f8727e_0
mkl_fft 1.3.1 py38hd3c417c_0
mkl_random 1.2.2 py38h51133e4_0
ncurses 6.4 h6a678d5_0
networkx 3.1 pypi_0 pypi
numba 0.56.4 py38h417a72b_0
numcodecs 0.12.1 pypi_0 pypi
numpy 1.21.6 pypi_0 pypi
numpy-base 1.23.5 py38h31eccc5_0
ome-types 0.4.3 pypi_0 pypi
opencv-python 4.8.1.78 pypi_0 pypi
openssl 1.1.1l h7f98852_0 conda-forge
packaging 23.2 pypi_0 pypi
pandas 2.0.3 pypi_0 pypi
partd 1.4.1 pypi_0 pypi
pillow 10.1.0 pypi_0 pypi
pint 0.21.1 pypi_0 pypi
pip 23.3.1 py38h06a4308_0
psutil 5.9.6 pypi_0 pypi
pydantic 2.5.2 pypi_0 pypi
pydantic-compat 0.1.2 pypi_0 pypi
pydantic-core 2.14.5 pypi_0 pypi
pyparsing 3.1.1 pypi_0 pypi
pysocks 1.7.1 pypi_0 pypi
python 3.8.0 h0371630_2
python-bioformats 4.0.7 pypi_0 pypi
python-dateutil 2.8.2 pypi_0 pypi
pytz 2023.3.post1 pypi_0 pypi
pywavelets 1.4.1 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
readline 7.0 h7b6447c_5
requests 2.31.0 pypi_0 pypi
resource-backed-dask-array 0.1.0 pypi_0 pypi
scikit-image 0.21.0 pypi_0 pypi
scikit-learn 1.0.2 pypi_0 pypi
scipy 1.10.1 pypi_0 pypi
scyjava 1.9.1 pypi_0 pypi
setuptools 68.0.0 py38h06a4308_0
six 1.16.0 pyhd3eb1b0_1
soupsieve 2.5 pypi_0 pypi
sqlite 3.33.0 h62c20be_0
tbb 2021.8.0 hdb19cb5_0
threadpoolctl 3.2.0 pypi_0 pypi
tifffile 2023.7.10 pypi_0 pypi
tk 8.6.12 h1ccaba5_0
toolz 0.12.0 pypi_0 pypi
tqdm 4.66.1 pypi_0 pypi
typing-extensions 4.8.0 pypi_0 pypi
tzdata 2023.3 pypi_0 pypi
urllib3 2.1.0 pypi_0 pypi
wheel 0.41.2 py38h06a4308_0
wrapt 1.16.0 pypi_0 pypi
xarray 2023.1.0 pypi_0 pypi
xmlschema 2.5.0 pypi_0 pypi
xmltodict 0.13.0 py38h06a4308_0
xsdata 23.8 pypi_0 pypi
xz 5.4.5 h5eee18b_0
zarr 2.16.1 pypi_0 pypi
zipp 3.17.0 pypi_0 pypi
zlib 1.2.13 h5eee18b_0