Wrong image dimensions Convert .mcd files to .ome.tiff files

[mousavinejhad]

Hello,

I have followed the steps in the link below and ran the pipeline as described at https://bodenmillergroup.github.io/ImcSegmentationPipeline/. I am attempting to run the “imc_preprocessing.ipynb” notebook to reproduce the results from the "Patient1"-"Patient4" raw data example provided in your GitHub repository. It appears that the code has successfully read the data from the “raw” directory and populated the files into the “/analysis/ometiff” folder. However, at a later stage, when attempting to “Convert -ome.tiff files to histoCAT compatible format,” I encounter the following error:

‹tifffile.TiffFile 'Patient1_s0_a3_ac.ome.tiff'> OME series cannot handle discontiguous storage ((600, 1) != (600, 600))

I have attempted to downgrade the version of tifffile as outlined below, but unfortunately, it did not resolve the issue:

pip uninstall tifffile
pip install tifffile==2023.4.12

Also, here is the output of !conda list

packages in environment at /opt/anaconda3/envs/imcsegpipe:

Name Version Build Channel

anyio 4.6.2.post1 pyhd8ed1ab_0 conda-forge
appnope 0.1.4 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39h06df861_5 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 24.2.0 pyh71513ae_0 conda-forge
babel 2.16.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
bleach 6.2.0 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py39hfa9831e_2 conda-forge
bzip2 1.0.8 h99b78c6_7 conda-forge
ca-certificates 2024.8.30 hf0a4a13_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py39h7f933ea_0 conda-forge
charset-normalizer 3.4.0 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
debugpy 1.8.9 py39h941272d_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge
executing 2.1.0 pyhd8ed1ab_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.7 pyh29332c3_1 conda-forge
httpx 0.28.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
idna 3.10 pyhd8ed1ab_0 conda-forge
imageio 2.36.1 pypi_0 pypi
imcsegpipe 1.0.0 pypi_0 pypi
importlib-metadata 8.5.0 pyha770c72_0 conda-forge
importlib_resources 6.4.5 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.5 pyh57ce528_0 conda-forge
ipython 8.18.1 pyh707e725_3 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.2 pyhff2d567_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
json5 0.10.0 pyhd8ed1ab_0 conda-forge
jsonpointer 3.0.0 py39h2804cbe_1 conda-forge
jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2024.10.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.23.0 hd8ed1ab_0 conda-forge
jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.14.2 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge
jupyterlab 4.3.1 pyhff2d567_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge
jupyterlab_server 2.27.3 pyhd8ed1ab_0 conda-forge
jupytext 1.16.4 pyh80e38bb_0 conda-forge
krb5 1.21.3 h237132a_0 conda-forge
libcxx 19.1.4 ha82da77_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libsodium 1.0.20 h99b78c6_0 conda-forge
libsqlite 3.47.0 hbaaea75_1 conda-forge
libzlib 1.3.1 h8359307_2 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 3.0.2 py39h66d85bf_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mdit-py-plugins 0.4.2 pyhd8ed1ab_0 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
nbclient 0.10.1 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.4 pyhd8ed1ab_1 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
ncurses 6.5 h7bae524_1 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge
numpy 2.0.2 pypi_0 pypi
openssl 3.4.0 h39f12f2_0 conda-forge
overrides 7.7.0 pyhd8ed1ab_0 conda-forge
packaging 24.2 pyhff2d567_1 conda-forge
pandas 2.2.3 pypi_0 pypi
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 11.0.0 pypi_0 pypi
pip 24.3.1 pyh8b19718_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_0 conda-forge
prometheus_client 0.21.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.48 pyha770c72_0 conda-forge
psutil 6.1.0 py39h57695bc_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pyobjc-core 10.3.1 py39hdc109a9_1 conda-forge
pyobjc-framework-cocoa 10.3.1 py39hdc109a9_1 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.20 h9e33284_1_cpython conda-forge
python-dateutil 2.9.0.post0 pyhff2d567_0 conda-forge
python-fastjsonschema 2.21.0 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python_abi 3.9 5_cp39 conda-forge
pytz 2024.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py39h06df861_1 conda-forge
pyzmq 26.2.0 py39h6e893d0_3 conda-forge
readimc 0.8.0 pypi_0 pypi
readline 8.2 h92ec313_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rpds-py 0.21.0 py39hc40b5db_0 conda-forge
scipy 1.13.1 pypi_0 pypi
send2trash 1.8.3 pyh31c8845_0 conda-forge
setuptools 75.6.0 pyhff2d567_1 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyh31c8845_0 conda-forge
tifffile 2024.8.30 pypi_0 pypi
tinycss2 1.4.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 h5083fa2_1 conda-forge
tomli 2.2.1 pyhd8ed1ab_0 conda-forge
tornado 6.4.2 py39hf3bc14e_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20241003 pyhff2d567_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2024.2 pypi_0 pypi
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.2.3 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 24.8.0 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.8.0 pyhd8ed1ab_1 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xtiff 0.7.9 pypi_0 pypi
xz 5.2.6 h57fd34a_0 conda-forge
yaml 0.2.5 h3422bc3_2 conda-forge
zeromq 4.3.5 hc1bb282_7 conda-forge
zipp 3.21.0 pyhd8ed1ab_1 conda-forge
zstandard 0.23.0 py39hcf1bb16_1 conda-forge
zstd 1.5.6 hb46c0d2_0 conda-forge

Any help and advice to resolve the issue would be greatly appreciated.

Many thanks