Image Stacks Generation - Key Error

[Guille916]

Hi, thanks for the Pipeline. It's been very helpfull so far!

I get this Key Error in the Image Stacks Generation step! Don't have much experience and don't know why. Hope you could help me out please!

[nilseling]

Hi @Guille916

Could you please add a screenshot of the first code chunk of the script and a screenshot of your panel file?

[Guille916]

Hi @nilseling

Thanks for the quick response! Here you go..

[nilseling]

Hmm, that does look correct to me. @jwindhager could you quickly check if I'm missing anything?

[jwindhager]

@nilseling LGTM. Maybe check whether the correct panel file is being loaded (e.g. csv vs xlsx or other formats, directory, ...)?

[nilseling]

Hi @Guille916, would it be possible if you shared a single MCD file and the panel file with me (nils.eling@uzh.ch)?

[Guille916]

Hi @nilseling, I just sent them to your email!

Thanks,

[nilseling]

Perfect, thanks! I'll take a look at it tonight and will come back to you asap

[nilseling]

Hey @Guille916 thanks for sharing the data! Looking at your panel file you use ; as separator instead of ,. I haven't gotten access yet to the MCD but could you try saving the panel as comma-separated CSV and test again?

[Guille916]

Many thanks @nilseling I did the change about the comma-separated that you suggested me, and it seems to work. I have another message (Here the screenshot), not sure of its meaning...

Thank you very much for your quick help and response on this matter!

Cheers,
Guille

[nilseling]

Hi @Guille916

I was not able to reproduce this error on my side. You could remove the current conda environment (conda env remove -n imcsegpipe) and build it again? You should get a new warning (see #122) but you can safely ignore it.

[Guille916]

Hi @nilseling Will do. Thank you for all the help!

Cheers,
Guille

[Guille916]

Hi @nilseling I removed the current conda environment and built it again, but still got the same warning...do you think I should worry or just move ahead?

Best,
Guille

[nilseling]

Could you please open the generated TIFF files in FIJI and check if they are correct? And could you also please add the output of !conda list here?

[Guille916]

Thank you @nilseling
I wasn't able to open any TIFF file from the cpout/images directory (full.tiff) Please see screenshot. But I was able to open TIFF files from the ilsatik repository (ilastik.tiff) and they look ok.

Here's the output of !conda list:

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

Name Version Build Channel

aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge
aiosqlite 0.18.0 pyhd8ed1ab_0 conda-forge
anyio 3.6.2 pyhd8ed1ab_0 conda-forge
appnope 0.1.3 pyhd8ed1ab_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py39ha30fb19_3 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
attrs 22.2.0 pyh71513ae_0 conda-forge
babel 2.11.0 pyhd8ed1ab_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 pyhd8ed1ab_3 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.2 pyha770c72_0 conda-forge
bleach 6.0.0 pyhd8ed1ab_0 conda-forge
brotlipy 0.7.0 py39ha30fb19_1005 conda-forge
bzip2 1.0.8 h0d85af4_4 conda-forge
ca-certificates 2022.12.7 h033912b_0 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py39h131948b_3 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
comm 0.1.2 pyhd8ed1ab_0 conda-forge
cryptography 39.0.1 py39hbeae22c_0 conda-forge
debugpy 1.6.6 py39h7a8716b_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
executing 1.2.0 pyhd8ed1ab_0 conda-forge
flit-core 3.8.0 pyhd8ed1ab_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
imageio 2.25.1 pypi_0 pypi
imcsegpipe 1.0.0 pypi_0 pypi
importlib-metadata 6.0.0 pyha770c72_0 conda-forge
importlib_metadata 6.0.0 hd8ed1ab_0 conda-forge
importlib_resources 5.10.2 pyhd8ed1ab_0 conda-forge
ipykernel 6.21.2 pyh736e0ef_0 conda-forge
ipython 8.10.0 pyhd1c38e8_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jedi 0.18.2 pyhd8ed1ab_0 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge
jupyter_client 8.0.2 pyhd8ed1ab_0 conda-forge
jupyter_core 5.2.0 py39h6e9494a_0 conda-forge
jupyter_events 0.5.0 pyhd8ed1ab_1 conda-forge
jupyter_server 2.3.0 pyhd8ed1ab_0 conda-forge
jupyter_server_fileid 0.6.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge
jupyter_server_ydoc 0.6.1 pyhd8ed1ab_0 conda-forge
jupyter_ydoc 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab 3.6.1 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
jupyterlab_server 2.19.0 pyhd8ed1ab_0 conda-forge
jupytext 1.14.4 pyhcff175f_0 conda-forge
libcxx 14.0.6 hccf4f1f_0 conda-forge
libffi 3.4.2 h0d85af4_5 conda-forge
libsodium 1.0.18 hbcb3906_1 conda-forge
libsqlite 3.40.0 ha978bb4_0 conda-forge
libzlib 1.2.13 hfd90126_4 conda-forge
markdown-it-py 2.1.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.2 py39ha30fb19_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mdit-py-plugins 0.3.3 pyhd8ed1ab_0 conda-forge
mdurl 0.1.0 pyhd8ed1ab_0 conda-forge
mistune 2.0.5 pyhd8ed1ab_0 conda-forge
nbclassic 0.5.1 pyhd8ed1ab_0 conda-forge
nbclient 0.7.2 pyhd8ed1ab_0 conda-forge
nbconvert 7.2.9 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.2.9 pyhd8ed1ab_0 conda-forge
nbconvert-pandoc 7.2.9 pyhd8ed1ab_0 conda-forge
nbformat 5.7.3 pyhd8ed1ab_0 conda-forge
ncurses 6.3 h96cf925_1 conda-forge
nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge
notebook 6.5.2 pyha770c72_1 conda-forge
notebook-shim 0.2.2 pyhd8ed1ab_0 conda-forge
numpy 1.24.2 pypi_0 pypi
openssl 3.0.8 hfd90126_0 conda-forge
packaging 23.0 pyhd8ed1ab_0 conda-forge
pandas 1.5.3 pypi_0 pypi
pandoc 2.19.2 h694c41f_1 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pexpect 4.8.0 pyh1a96a4e_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.4.0 pypi_0 pypi
pip 23.0 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge
platformdirs 3.0.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.36 pyha770c72_0 conda-forge
psutil 5.9.4 py39ha30fb19_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.14.0 pyhd8ed1ab_0 conda-forge
pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge
pyrsistent 0.19.3 py39ha30fb19_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.16 h709bd14_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.16.2 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.6 pyhd8ed1ab_0 conda-forge
python_abi 3.9 3_cp39 conda-forge
pytz 2022.7.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py39ha30fb19_5 conda-forge
pyzmq 25.0.0 py39hed8f129_0 conda-forge
readimc 0.6.2 pypi_0 pypi
readline 8.1.2 h3899abd_0 conda-forge
requests 2.28.2 pyhd8ed1ab_0 conda-forge
scipy 1.10.0 pypi_0 pypi
send2trash 1.8.0 pyhd8ed1ab_0 conda-forge
setuptools 67.3.1 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.0 pyhd8ed1ab_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
terminado 0.17.1 pyhd1c38e8_0 conda-forge
tifffile 2023.2.3 pypi_0 pypi
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h5dbffcc_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.2 py39ha30fb19_1 conda-forge
traitlets 5.9.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.4.0 hd8ed1ab_0 conda-forge
typing_extensions 4.4.0 pyha770c72_0 conda-forge
tzdata 2022g h191b570_0 conda-forge
urllib3 1.26.14 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge
wheel 0.38.4 pyhd8ed1ab_0 conda-forge
xtiff 0.7.9 pypi_0 pypi
xz 5.2.6 h775f41a_0 conda-forge
y-py 0.5.5 py39hd4bc93a_2 conda-forge
yaml 0.2.5 h0d85af4_2 conda-forge
ypy-websocket 0.8.2 pyhd8ed1ab_0 conda-forge
zeromq 4.3.4 he49afe7_1 conda-forge
zipp 3.13.0 pyhd8ed1ab_0 conda-forge

[nilseling]

Hmm, these are the same package version I'm using on my side. Is the affected file the one you send me?

[Guille916]

Hmm, yes it is. It seems that the TIFF files from the ilastik folder (ilastik.tiff) are ok, but the ones in the cpout folder aren't (full.tiff). But not sure if this has something to do with the warning message..Not sure what else could be? Maybe try to remove and build the environment again?

Sorry for the trouble!

[nilseling]

Yes, the warning message tells you that empty TIFF files have been written out. Could you please to restart the python kernel and run all chunks again? There should be a button for this at the top.

[Guille916]

@nilseling Restarting the kernel did work! Now I have the full as well as the ilastick stacks!

Many thanks for your help!

Best,
Guille

[nilseling]

Excellent :) I will close this issue now