QyQt6 error when using napariGater() + local fix #146
Description
I installed Scimap into a fresh environment and when using napariGater I got two errors:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
Cell In[27], line 1
----> 1 sm.pl.napariGater(image_path, adata, calculate_contrast= False)
File ~/anaconda3/envs/scimap_brainmets-env/lib/python3.10/site-packages/scimap/plotting/napariGater.py:524, in napariGater(image_path, adata, layer, log, x_coordinate, y_coordinate, imageid, subset, flip_y, channel_names, point_size, calculate_contrast, verbose)
521 hist_ax = hist_fig.add_subplot(111)
523 # QLabel to show the gate threshold outside the plot
--> 524 gate_label = QLabel("Gate Threshold: N/A")
525 gate_label.setAlignment(Qt.AlignCenter)
526 gate_label.setStyleSheet("color: white; font-size: 15pt; padding-top: 1px;")
NameError: name 'QLabel' is not defined
And
Warning: Could not determine data range for ICAM1, using defaults. Error: <COMPRESSION.LZW: 5> requires the 'imagecodecs' package
I installed Scimap with pip install "scimap[napari]" and additionally pip install imagecodecs.
I was able to fix it locally by going into ~/anaconda3/envs/scimap_brainmets-env/lib/python3.10/site-packages/scimap/plotting/napariGater.py and changing
from PyQt5.QtWidgets import QLabel
from PyQt5.QtCore import Qt
to importing from PyQt6. As scimap automatically installs with pyqt6 this problem may be arising for other people as well. Is it possible to solve this already at the source to avoid the local fix?
I am on a M2 Mac and this is the content of my Conda environment:
# packages in environment at /Users/margotchazotte/anaconda3/envs/scimap_brainmets-env:
#
# Name Version Build Channel
aiobotocore 3.1.2 pypi_0 pypi
aiohappyeyeballs 2.6.1 pypi_0 pypi
aiohttp 3.13.3 pypi_0 pypi
aioitertools 0.13.0 pypi_0 pypi
aiosignal 1.4.0 pypi_0 pypi
alabaster 1.0.0 pypi_0 pypi
anndata 0.10.9 pypi_0 pypi
annotated-doc 0.0.4 pypi_0 pypi
annotated-types 0.7.0 pypi_0 pypi
app-model 0.2.8 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
appnope 0.1.4 pypi_0 pypi
array-api-compat 1.13.0 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
asttokens 3.0.1 pypi_0 pypi
async-timeout 5.0.1 pypi_0 pypi
attrs 25.4.0 pypi_0 pypi
babel 2.18.0 pypi_0 pypi
backrefs 6.1 pypi_0 pypi
botocore 1.42.42 pypi_0 pypi
build 1.4.0 pypi_0 pypi
bzip2 1.0.8 h80987f9_6
ca-certificates 2025.12.2 hca03da5_0
cachey 0.2.1 pypi_0 pypi
certifi 2026.1.4 pypi_0 pypi
charset-normalizer 3.4.4 pypi_0 pypi
click 8.3.1 pypi_0 pypi
cloudpickle 3.1.2 pypi_0 pypi
colorama 0.4.6 pypi_0 pypi
combat 0.3.3 pypi_0 pypi
comm 0.2.3 pypi_0 pypi
contourpy 1.3.2 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
dask 2023.12.1 pypi_0 pypi
debugpy 1.8.20 pypi_0 pypi
decorator 5.2.1 pypi_0 pypi
docstring-parser 0.17.0 pypi_0 pypi
docutils 0.21.2 pypi_0 pypi
exceptiongroup 1.3.1 pypi_0 pypi
executing 2.2.1 pypi_0 pypi
expat 2.7.4 h50f4ffc_0
fast-histogram 0.14 pypi_0 pypi
fasteners 0.20 pypi_0 pypi
flexcache 0.3 pypi_0 pypi
flexparser 0.4 pypi_0 pypi
fonttools 4.61.1 pypi_0 pypi
freetype-py 2.5.1 pypi_0 pypi
frozenlist 1.8.0 pypi_0 pypi
fsspec 2026.2.0 pypi_0 pypi
gensim 4.4.0 pypi_0 pypi
ghp-import 2.1.0 pypi_0 pypi
h5py 3.15.1 pypi_0 pypi
heapdict 1.0.1 pypi_0 pypi
hsluv 5.0.4 pypi_0 pypi
idna 3.11 pypi_0 pypi
igraph 1.0.0 pypi_0 pypi
imagecodecs 2025.3.30 pypi_0 pypi
imageio 2.37.2 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
importlib-metadata 8.7.1 pypi_0 pypi
in-n-out 0.2.1 pypi_0 pypi
iniconfig 2.3.0 pypi_0 pypi
ipykernel 6.31.0 pypi_0 pypi
ipython 8.38.0 pypi_0 pypi
ipython-pygments-lexers 1.1.1 pypi_0 pypi
ipywidgets 8.1.8 pypi_0 pypi
jedi 0.19.2 pypi_0 pypi
jinja2 3.1.6 pypi_0 pypi
jmespath 1.1.0 pypi_0 pypi
joblib 1.5.3 pypi_0 pypi
jsonschema 4.26.0 pypi_0 pypi
jsonschema-specifications 2025.9.1 pypi_0 pypi
jupyter-client 8.8.0 pypi_0 pypi
jupyter-core 5.9.1 pypi_0 pypi
jupyterlab-widgets 3.0.16 pypi_0 pypi
kiwisolver 1.4.9 pypi_0 pypi
lazy-loader 0.4 pypi_0 pypi
legacy-api-wrap 1.5 pypi_0 pypi
leidenalg 0.11.0 pypi_0 pypi
libcxx 21.1.8 hb4ce287_0
libexpat 2.7.4 h50f4ffc_0
libffi 3.4.4 hca03da5_1
libzlib 1.3.1 h5f15de7_0
llvmlite 0.41.1 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
magicgui 0.10.1 pypi_0 pypi
markdown 3.10.2 pypi_0 pypi
markdown-it-py 4.0.0 pypi_0 pypi
markupsafe 3.0.3 pypi_0 pypi
matplotlib 3.10.8 pypi_0 pypi
matplotlib-inline 0.2.1 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
mergedeep 1.3.4 pypi_0 pypi
mkdocs 1.6.1 pypi_0 pypi
mkdocs-get-deps 0.2.0 pypi_0 pypi
mkdocs-material 9.7.1 pypi_0 pypi
mkdocs-material-extensions 1.3.1 pypi_0 pypi
mpl-scatter-density 0.7 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
multidict 6.7.1 pypi_0 pypi
napari 0.4.19.post1 pypi_0 pypi
napari-console 0.1.4 pypi_0 pypi
napari-ome-zarr 0.4.0 pypi_0 pypi
napari-plugin-engine 0.2.1 pypi_0 pypi
napari-svg 0.2.1 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
ncurses 6.5 hee39554_0
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.4.2 pypi_0 pypi
npe2 0.8.1 pypi_0 pypi
numba 0.58.1 pypi_0 pypi
numcodecs 0.13.1 pypi_0 pypi
numpy 1.26.4 pypi_0 pypi
numpydoc 1.10.0 pypi_0 pypi
ome-zarr 0.11.1 pypi_0 pypi
openssl 3.0.19 ha0b305a_0
packaging 25.0 py310hca03da5_1
paginate 0.5.7 pypi_0 pypi
pandas 2.3.3 pypi_0 pypi
parso 0.8.6 pypi_0 pypi
partd 1.4.2 pypi_0 pypi
pathspec 1.0.4 pypi_0 pypi
patsy 1.0.2 pypi_0 pypi
pexpect 4.9.0 pypi_0 pypi
phenograph 1.5.7 pypi_0 pypi
pillow 12.1.1 pypi_0 pypi
pint 0.24.4 pypi_0 pypi
pip 26.0.1 pyhc872135_0
platformdirs 4.5.1 pypi_0 pypi
plotly 5.24.1 pypi_0 pypi
pluggy 1.6.0 pypi_0 pypi
pooch 1.9.0 pypi_0 pypi
prompt-toolkit 3.0.52 pypi_0 pypi
propcache 0.4.1 pypi_0 pypi
psutil 7.2.2 pypi_0 pypi
psygnal 0.15.1 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.3 pypi_0 pypi
pyconify 0.2.1 pypi_0 pypi
pydantic 2.12.5 pypi_0 pypi
pydantic-compat 0.1.2 pypi_0 pypi
pydantic-core 2.41.5 pypi_0 pypi
pydantic-extra-types 2.11.0 pypi_0 pypi
pygments 2.19.2 pypi_0 pypi
pymdown-extensions 10.20.1 pypi_0 pypi
pynndescent 0.6.0 pypi_0 pypi
pyopengl 3.1.10 pypi_0 pypi
pyparsing 3.3.2 pypi_0 pypi
pyproject-hooks 1.2.0 pypi_0 pypi
pyqt6 6.10.2 pypi_0 pypi
pyqt6-qt6 6.10.2 pypi_0 pypi
pyqt6-sip 13.11.0 pypi_0 pypi
pytest 7.4.4 pypi_0 pypi
pytest-xvfb 3.1.1 pypi_0 pypi
python 3.10.19 hf701271_0
python-dateutil 2.9.0.post0 pypi_0 pypi
pytz 2025.2 pypi_0 pypi
pyvirtualdisplay 3.0 pypi_0 pypi
pyyaml 6.0.3 pypi_0 pypi
pyyaml-env-tag 1.1 pypi_0 pypi
pyzmq 27.1.0 pypi_0 pypi
qtconsole 5.7.1 pypi_0 pypi
qtpy 2.4.3 pypi_0 pypi
readline 8.3 h0b18652_0
referencing 0.37.0 pypi_0 pypi
requests 2.32.5 pypi_0 pypi
rich 14.3.2 pypi_0 pypi
rpds-py 0.30.0 pypi_0 pypi
s3fs 2026.2.0 pypi_0 pypi
scanpy 1.11.5 pypi_0 pypi
scikit-image 0.25.2 pypi_0 pypi
scikit-learn 1.7.2 pypi_0 pypi
scimap 2.3.5 pypi_0 pypi
scipy 1.12.0 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
session-info2 0.4 pypi_0 pypi
setuptools 80.10.2 py310hca03da5_0
shapely 2.1.2 pypi_0 pypi
shellingham 1.5.4 pypi_0 pypi
six 1.17.0 pypi_0 pypi
smart-open 7.5.0 pypi_0 pypi
snowballstemmer 3.0.1 pypi_0 pypi
sphinx 8.1.3 pypi_0 pypi
sphinxcontrib-applehelp 2.0.0 pypi_0 pypi
sphinxcontrib-devhelp 2.0.0 pypi_0 pypi
sphinxcontrib-htmlhelp 2.1.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 2.0.0 pypi_0 pypi
sphinxcontrib-serializinghtml 2.0.0 pypi_0 pypi
sqlite 3.51.1 hab6afd1_0
stack-data 0.6.3 pypi_0 pypi
statsmodels 0.14.6 pypi_0 pypi
superqt 0.7.8 pypi_0 pypi
tenacity 9.1.4 pypi_0 pypi
texttable 1.7.0 pypi_0 pypi
threadpoolctl 3.6.0 pypi_0 pypi
tifffile 2023.12.9 pypi_0 pypi
tk 8.6.15 hcd8a7d5_0
tomli 2.4.0 pypi_0 pypi
tomli-w 1.2.0 pypi_0 pypi
toolz 1.1.0 pypi_0 pypi
tornado 6.5.4 pypi_0 pypi
tqdm 4.67.3 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
typer 0.22.0 pypi_0 pypi
typing-extensions 4.15.0 pypi_0 pypi
typing-inspection 0.4.2 pypi_0 pypi
tzdata 2025.3 pypi_0 pypi
umap-learn 0.5.11 pypi_0 pypi
urllib3 2.6.3 pypi_0 pypi
vispy 0.14.3 pypi_0 pypi
watchdog 6.0.0 pypi_0 pypi
wcwidth 0.6.0 pypi_0 pypi
wheel 0.46.3 py310hca03da5_0
widgetsnbextension 4.0.15 pypi_0 pypi
wrapt 2.1.1 pypi_0 pypi
xz 5.6.4 h80987f9_1
yarl 1.22.0 pypi_0 pypi
zarr 2.10.3 pypi_0 pypi
zipp 3.23.0 pypi_0 pypi
zlib 1.3.1 h5f15de7_0