MouseLand
BUG in drawing the areas
Hi,
I am trying to retrain a model and when I correct the mask as It IS explained in the tutorial video there is a point where I acnot correct anymore the mask and It start appearing points where I go with the pc mice.
In the conda prompt i have this result for each points.
QGraphicsScene::removeItem: item 0x2975b49cf80's scene (0x0) is different from this scene (0x2975de98860)
Anyone can help me???
Thanks
Dear Cellpose team, we are also encountering this same problem in the cellpose3 version. Are there any updates on this issue?
In brief, what we have experienced: While correcting manually a 2D mask by re-drawing labels, it often occurs that the starting-point of a newly started label disappears (red dot), and the label cannot be closed. So it keeps drawing the label and nothing can be done. The only way we found to exit the situation is to close cellpose and re-start it.
It would be great to get hints or help on this!
Thanks
Hi I have been facing the same issue and would be very grateful for any help or suggestions.
Thank you.
Hi, we are also experiencing the same problem. It sometimes gets so bad that it's not even possible to draw one label. Any help or suggestions would be really appreciated. Thanks!
Can you please share your OS and pip list? I know this happens on Mac but cannot replicate on other OS's
We are using LINUX, in the screenshot is the error message we get, and here below is the pip list
Package Version
------------------------ ---------
Brotli 1.1.0
cachetools 5.3.3
cellpose 3.0.7
certifi 2024.2.2
charset-normalizer 3.3.2
fastremap 1.14.1
filelock 3.13.1
fsspec 2024.3.1
gmpy2 2.1.2
google-api-core 2.18.0
google-auth 2.29.0
google-cloud-core 2.4.1
google-cloud-storage 2.16.0
google-crc32c 1.5.0
google-resumable-media 2.7.0
googleapis-common-protos 1.63.0
idna 3.6
imagecodecs 2023.3.16
importlib_metadata 7.1.0
Jinja2 3.1.3
llvmlite 0.41.1
MarkupSafe 2.1.5
mpmath 1.3.0
natsort 8.4.0
networkx 3.1
numba 0.58.1
numpy 1.24.4
opencv-python-headless 4.9.0.80
packaging 24.0
Pillow 9.4.0
pip 24.0
proto-plus 1.23.0
protobuf 4.25.3
pyasn1 0.5.1
pyasn1-modules 0.3.0
Pygments 2.17.2
PyQt6 6.6.1
PyQt6-Qt6 6.6.2
PyQt6-sip 13.6.0
pyqtgraph 0.13.3
PySocks 1.7.1
PyYAML 6.0.1
QtPy 2.4.1
requests 2.31.0
roifile 2023.5.12
rsa 4.9
scipy 1.10.1
setuptools 69.2.0
superqt 0.6.2
sympy 1.12
tifffile 2023.7.10
torch 2.2.1
torchaudio 2.2.1
torchvision 0.17.1
tqdm 4.66.2
triton 2.2.0
typing_extensions 4.10.0
urllib3 2.2.1
wheel 0.43.0
zipp 3.18.1
thanks can you please post your "conda list" as well? I can't reproduce this on windows and linux with the latest pyqt6 and pyqtgraph, and python=3.10 or python=3.11.
Thanks for answering, here is the conda list:
(cellpose3) akhan@jupyter-akhan:/home/akhan$ conda list
# packages in environment at /g/cba/miniconda3/envs/cellpose3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
blas 2.116 mkl conda-forge
blas-devel 3.9.0 16_linux64_mkl conda-forge
brotli-python 1.1.0 py38h17151c0_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cachetools 5.3.3 pypi_0 pypi
cellpose 3.0.7 pypi_0 pypi
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
cuda-cudart 11.8.89 0 nvidia
cuda-cupti 11.8.87 0 nvidia
cuda-libraries 11.8.0 0 nvidia
cuda-nvrtc 11.8.89 0 nvidia
cuda-nvtx 11.8.86 0 nvidia
cuda-runtime 11.8.0 0 nvidia
fastremap 1.14.1 pypi_0 pypi
ffmpeg 4.3 hf484d3e_0 pytorch
filelock 3.13.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fsspec 2024.3.1 pypi_0 pypi
gmp 6.3.0 h59595ed_1 conda-forge
gmpy2 2.1.2 py38h793c122_1 conda-forge
gnutls 3.6.13 h85f3911_1 conda-forge
google-api-core 2.18.0 pypi_0 pypi
google-auth 2.29.0 pypi_0 pypi
google-cloud-core 2.4.1 pypi_0 pypi
google-cloud-storage 2.16.0 pypi_0 pypi
google-crc32c 1.5.0 pypi_0 pypi
google-resumable-media 2.7.0 pypi_0 pypi
googleapis-common-protos 1.63.0 pypi_0 pypi
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
imagecodecs 2023.3.16 pypi_0 pypi
importlib-metadata 7.1.0 pypi_0 pypi
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
jpeg 9e h166bdaf_2 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.15 hfd0df8a_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libblas 3.9.0 16_linux64_mkl conda-forge
libcblas 3.9.0 16_linux64_mkl conda-forge
libcublas 11.11.3.6 0 nvidia
libcufft 10.9.0.58 0 nvidia
libcufile 1.9.0.20 0 nvidia
libcurand 10.3.5.119 0 nvidia
libcusolver 11.4.1.48 0 nvidia
libcusparse 11.7.5.86 0 nvidia
libdeflate 1.17 h0b41bf4_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgfortran-ng 13.2.0 h69a702a_5 conda-forge
libgfortran5 13.2.0 ha4646dd_5 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libhwloc 2.9.3 default_h554bfaf_1009 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 2.0.0 h9bf148f_0 pytorch
liblapack 3.9.0 16_linux64_mkl conda-forge
liblapacke 3.9.0 16_linux64_mkl conda-forge
libnpp 11.8.0.86 0 nvidia
libnsl 2.0.1 hd590300_0 conda-forge
libnvjpeg 11.9.0.86 0 nvidia
libpng 1.6.43 h2797004_0 conda-forge
libsqlite 3.45.2 h2797004_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libtiff 4.5.0 h6adf6a1_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.6 h232c23b_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
llvm-openmp 15.0.7 h0cdce71_0 conda-forge
llvmlite 0.41.1 pypi_0 pypi
markupsafe 2.1.5 py38h01eb140_0 conda-forge
mkl 2022.1.0 h84fe81f_915 conda-forge
mkl-devel 2022.1.0 ha770c72_916 conda-forge
mkl-include 2022.1.0 h84fe81f_915 conda-forge
mpc 1.3.1 hfe3b2da_0 conda-forge
mpfr 4.2.1 h9458935_0 conda-forge
mpmath 1.3.0 pyhd8ed1ab_0 conda-forge
natsort 8.4.0 pypi_0 pypi
ncurses 6.4.20240210 h59595ed_0 conda-forge
nettle 3.6 he412f7d_0 conda-forge
networkx 3.1 pyhd8ed1ab_0 conda-forge
numba 0.58.1 pypi_0 pypi
numpy 1.24.4 py38h59b608b_0 conda-forge
opencv-python-headless 4.9.0.80 pypi_0 pypi
openh264 2.1.1 h780b84a_0 conda-forge
openjpeg 2.5.0 hfec8fc6_2 conda-forge
openssl 3.2.1 hd590300_1 conda-forge
packaging 24.0 pypi_0 pypi
pillow 9.4.0 py38hde6dc18_1 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
proto-plus 1.23.0 pypi_0 pypi
protobuf 4.25.3 pypi_0 pypi
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyasn1 0.5.1 pypi_0 pypi
pyasn1-modules 0.3.0 pypi_0 pypi
pygments 2.17.2 pypi_0 pypi
pyqt6 6.6.1 pypi_0 pypi
pyqt6-qt6 6.6.2 pypi_0 pypi
pyqt6-sip 13.6.0 pypi_0 pypi
pyqtgraph 0.13.3 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.8.19 hd12c33a_0_cpython conda-forge
python_abi 3.8 4_cp38 conda-forge
pytorch 2.2.1 py3.8_cuda11.8_cudnn8.7.0_0 pytorch
pytorch-cuda 11.8 h7e8668a_5 pytorch
pytorch-mutex 1.0 cuda pytorch
pyyaml 6.0.1 py38h01eb140_1 conda-forge
qtpy 2.4.1 pypi_0 pypi
readline 8.2 h8228510_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
roifile 2023.5.12 pypi_0 pypi
rsa 4.9 pypi_0 pypi
scipy 1.10.1 pypi_0 pypi
setuptools 69.2.0 pyhd8ed1ab_0 conda-forge
superqt 0.6.2 pypi_0 pypi
sympy 1.12 pypyh9d50eac_103 conda-forge
tbb 2021.11.0 h00ab1b0_1 conda-forge
tifffile 2023.7.10 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
torchaudio 2.2.1 py38_cu118 pytorch
torchtriton 2.2.0 py38 pytorch
torchvision 0.17.1 py38_cu118 pytorch
tqdm 4.66.2 pypi_0 pypi
typing_extensions 4.10.0 pyha770c72_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zipp 3.18.1 pypi_0 pypi
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Thanks can you please see if this bug also happens in Python 3.9 or 3.10? We may need to deprecate 3.8, also update to the latest pyqt6 and pyqtgraph
another issue #997 , can you please try a later python version and the latest pyqt6 and pyqtgraph (pip install pyqt6 --upgrade ; pip install pyqtgraph --upgrade)
This is also happening to me in fresh enviroments with python versions of 3.8, 3.10 and 3.11
So that I can replicate your environment, please use this command and upload the yml: conda env export > environment.yml
Please do this in 3.10, is this in Windows or Linux?
This is on windows (seen issue in both windows 10 and windows server 2022). I've also included an image and seg.npy which for me will fairly consistently produce the bug when one or two new labels are added.
thank you @JamesWGrimshaw and @mayishazn for all the info about this bug, I was able to track it down, due to a squeeze of an axis that was causing an error but it was not printing any error. Also I was renumbering the masks and outlines during loading, and that could be inconsistent, so that is also now fixed (and the outlines will be recomputed for 2D images from seg files).
I can no longer reproduce the bug, but please let me know if you are still having issues.
install latest: pip install git+https://github.com/mouseland/cellpose.git
I created a new environment and did a fresh install. The red circle does disappear once I close the loop but it doesn't turn into a mask. I've drawn four here and they're just stuck with the purple dotted lines. There is no drawing related output in the terminal either.
@carsen-stringer I'm experiencing this issue with the latest version of cellpose. I created a fresh conda env with python 3.11 then only installed cellpose with pip install cellpose[gui]. Then after opening the GUI with cellpose --Zstack and checking the box for "single stroke", it will work for drawing maybe a few tens of cells then it seemingly randomly bugs out and won't let me close my shape any longer and I get repeated lines of this error message as I move the cursor:
QGraphicsScene::removeItem: item 0xd147550's scene (0x0) is different from this scene (0xc2625c0)
I've also tried updating to the latest dev release (3.1.1.2.dev7+g549126d) and downgrading to 2.3.2 and encountered the same problem. Downgrading to 2.2.3 seems to have solved it though.
