Incomplete masks

[qinghezeng]

Thank you for making public such fantastic codes!

When I ran the following command for my dataset,
python create_patches.py --source $SOURCE_DIR --save_dir $SAVE_DIR --patch_size 256 --seg

I got incomplete mask for some slides. Here is an example:

Could you please point out what I did wrong and how to fix it? Thank you!

[jjhbw]

Funny, I have the same issue. I don't think this is related to CLAM, though. Which OS are you using? I wasn't able to reproduce this on MacOS using the exact same codebase.

[qinghezeng]

Yeah that's funny... I am using Ubuntu 18. Do you have the same issue with Ubuntu?

[jjhbw]

Yes, this happens on Ubuntu for me.

I'm running a slightly different Conda environment than the one suggested by the CLAM docs:

certifi==2020.6.20
future==0.18.2
h5py==2.10.0
numpy==1.19.1
opencv-python==4.3.0.36
openslide-python @ git+https://github.com/openslide/openslide-python.git@3e9fbca4ea4e729756c6cf76f7bca87e3e8846d1
pandas==1.1.0
Pillow==7.2.0
python-dateutil==2.8.1
pytz==2020.1
scikit-learn==0.23.2
scipy==1.5.2
Shapely==1.6.4.post1
six==1.15.0
tensorboard==2.3.0
topk @ git+https://github.com/oval-group/smooth-topk.git@940ffa4b8d8e85e2eca1ec67220cc1ff13cd68f9
torch==1.6.0
torchvision==0.7.0

Speculating: i think this may be an OpenSlide or Pillow issue. Both come with platform-dependent binaries when installed, which may contain some weird bug.

Can you show your pip freeze output?

[qinghezeng]

Thank you for your reply! Here is my pip freeze output:

2to3==1.0
absl-py==0.9.0
asciitree==0.3.3
asgiref==2.3.2
asn1crypto==1.2.0
astor==0.8.0
async-timeout==3.0.1
atomicwrites==1.3.0
attrs==19.3.0
autobahn==19.5.1
Automat==0.8.0
backcall==0.1.0
bleach==3.1.0
certifi==2019.11.28
cffi==1.14.0
channels==2.1.7
chardet==3.0.4
Click==7.0
codacy-coverage==1.3.11
constantly==15.1.0
coverage==4.5.4
cryptography==2.3.1
cycler==0.10.0
Cython==0.29.15
daphne==2.2.5
decorator==4.4.2
defusedxml==0.6.0
Django==2.2.7
djangorestframework==3.9.4
entrypoints==0.3
fasteners==0.15
filelock==3.0.12
Flask==1.0.2
future==0.18.2
gast==0.3.3
google-pasta==0.2.0
grpcio==1.27.2
h5py==2.10.0
hyperlink==19.0.0
idna==2.8
imagecodecs==2020.2.18
imageio==2.6.1
importlib-metadata==1.5.0
incremental==17.5.0
intervaltree==3.0.2
ipykernel==5.1.4
ipython==7.13.0
ipython-genutils==0.2.0
itsdangerous==1.1.0
jedi==0.16.0
Jinja2==2.11.1
joblib==0.14.0
jsonfield2==3.0.3
jsonschema==2.6.0
jupyter-client==6.1.0
jupyter-core==4.6.1
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.0
kiwisolver==1.1.0
lmdb==0.98
lxml==4.2.1
lz4==2.2.1
Markdown==3.1.1
MarkupSafe==1.1.1
matplotlib==3.1.1
mistune==0.8.4
mkl-fft==1.0.15
mkl-random==1.1.0
mkl-service==2.3.0
monotonic==1.5
more-itertools==8.5.0
mypy-extensions==0.4.3
nbconvert==5.6.1
nbformat==5.0.4
ndg-httpsclient==0.5.0
networkx==2.4
notebook==6.0.1
numcodecs==0.6.4
numpy==1.18.1
olefile==0.46
opencv-python==4.1.1.26
openslide-python==1.1.1
openslides==3.0
packaging==19.2
pandas==0.25.3
pandocfilters==1.4.2
parso==0.6.2
pexpect==4.8.0
pickleshare==0.7.5
Pillow==7.0.0
pkgconfig==1.5.1
pluggy==0.13.1
progressbar2==3.43.1
prometheus-client==0.7.1
prompt-toolkit==3.0.4
protobuf==3.10.0
ptyprocess==0.6.0
py==1.8.0
pyasn1==0.4.3
pycparser==2.20
pyflann==1.6.14
Pygments==2.6.1
PyHamcrest==1.9.0
pyOpenSSL==18.0.0
pyparsing==2.4.6
PyPDF2==1.26.0
pyrsistent==0.15.7
pytest==4.6.2
pytest-cov==2.7.1
python-dateutil==2.8.1
python-utils==2.3.0
pytz==2019.3
PyWavelets==1.1.1
PyYAML==3.13
pyzmq==18.1.1
requests==2.22.0
requests-mock==1.5.2
roman==3.1
scikit-image==0.16.2
scikit-learn==0.22.1
scipy==1.4.1
seaborn==0.9.0
Send2Trash==1.5.0
six==1.14.0
sklearn==0.0
sortedcontainers==2.1.0
spams==2.6.1
sqlparse==0.3.0
tensorboard==1.14.0
tensorboardX==1.9
tensorflow==1.14.0
tensorflow-estimator==1.14.0
termcolor==1.1.0
terminado==0.8.3
testpath==0.4.4
tifffile==2020.2.16
toml==0.10.0
topk==1.0
torch==1.3.1
torchsummary==1.5.1
torchvision==0.1.8
tornado==6.0.4
tox==3.13.2
tqdm==4.37.0
traitlets==4.3.3
Twisted==19.7.0
txaio==18.8.1
typing-extensions==3.7.4.1
urllib3==1.25.7
virtualenv==16.7.7
wcwidth==0.1.8
webencodings==0.5.1
websockets==8.1
Werkzeug==1.0.0
wrapt==1.12.1
zarr==2.3.2
zipp==2.2.0
zope.interface==4.6.0

And my conda version is 4.8.3, Python version is 3.7.7.

[fedshyvana]

Hi all, after some digging around, yes, as far as I am aware of, this is an issue with pixman which Openslide uses. Specifically, I think pixman 0.38.x has this issue. If you either update pixman to 0.40.x or downgrade to 0.36.x this issue should go away.
You can download pixman from here

[fedshyvana]

More discussion about this can be found here although some of this thread might be a little outdated/inaccurate and would depend on your os and whether you're using conda or not.

[jjhbw]

Fantastic! Never would have thought of that. It always amazes me how deep the library dependency rabbit hole can go in modern software ecosystems, but I digress...

Maybe you can include the fix (conda install pixman == vx?) in the installation docs, to spare future users the headache? I don't have the time to dig deep into this, so I'm not sure that the fix is actually this easy...

[fedshyvana]

Yes i'm not sure a simple conda install pixman would fix it haha since apparently other libraries sometimes specify a dependency for specific versions of pixman as well. What worked for me was download pixman 0.40 from the link above, manually compile and install. And then for conda I manually copied libpixman-1.so.0.40 into the ~/anaconda/lib folder and ~/anaconda/envs/clam/lib folder to replace the old 0.38 version. Felt pretty hacky but it worked.
I will keep an eye out and update the installation doc if a proper fix for this comes out.

[jjhbw]

Ah wow, thanks for letting us know.. Always good to know what kind of debugging you can expect.

This doesn't sound good. At all. OpenSlide is beginning to look like an increasingly fundamental-yet-fragile part of the digital pathology ecosystem. Really hope some brave soul picks up its maintenance again soon.

[qinghezeng]

I agree with @fedshyvana

Yes i'm not sure a simple conda install pixman would fix it haha

I tried conda install pixman = 0.36.0 and conda install pixman = 0.40.0, and it gave me this error:

Solving environment: failed with initial frozen solve. Retrying with flexible solve.

Finally I fixed it by

manually copied libpixman-1.so.0.40 into the ~/anaconda/lib folder and ~/anaconda/envs/clam/lib folder to replace the old 0.38 version

Thank you so much for all your help!! @fedshyvana @jjhbw

[jjhbw]

For posterity: conda install -c anaconda pixman did the trick for me, as it installed pixman 0.40.0.

My conda list now looks like:

# packages in environment at /home/x/.conda/envs/x:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
absl-py                   0.10.0                   pypi_0    pypi
ca-certificates           2020.7.22                     0    anaconda
cachetools                4.1.1                    pypi_0    pypi
certifi                   2020.6.20                py37_0    anaconda
chardet                   3.0.4                    pypi_0    pypi
future                    0.18.2                   pypi_0    pypi
google-auth               1.20.1                   pypi_0    pypi
google-auth-oauthlib      0.4.1                    pypi_0    pypi
grpcio                    1.31.0                   pypi_0    pypi
h5py                      2.10.0                   pypi_0    pypi
idna                      2.10                     pypi_0    pypi
importlib-metadata        1.7.0                    pypi_0    pypi
joblib                    0.16.0                   pypi_0    pypi
ld_impl_linux-64          2.33.1               h53a641e_7  
libedit                   3.1.20191231         h14c3975_1  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 9.1.0                hdf63c60_0  
libstdcxx-ng              9.1.0                hdf63c60_0  
markdown                  3.2.2                    pypi_0    pypi
ncurses                   6.2                  he6710b0_1  
numpy                     1.19.1                   pypi_0    pypi
oauthlib                  3.1.0                    pypi_0    pypi
opencv-python             4.3.0.36                 pypi_0    pypi
openslide-python          1.1.1                    pypi_0    pypi
openssl                   1.1.1g               h7b6447c_0    anaconda
pandas                    1.1.0                    pypi_0    pypi
pillow                    7.2.0                    pypi_0    pypi
pip                       20.2.2                   py37_0  
pixman                    0.40.0               h7b6447c_0    anaconda
protobuf                  3.13.0                   pypi_0    pypi
pyasn1                    0.4.8                    pypi_0    pypi
pyasn1-modules            0.2.8                    pypi_0    pypi
python                    3.7.7                hcff3b4d_5  
python-dateutil           2.8.1                    pypi_0    pypi
pytz                      2020.1                   pypi_0    pypi
readline                  8.0                  h7b6447c_0  
requests                  2.24.0                   pypi_0    pypi
requests-oauthlib         1.3.0                    pypi_0    pypi
rsa                       4.6                      pypi_0    pypi
scikit-learn              0.23.2                   pypi_0    pypi
scipy                     1.5.2                    pypi_0    pypi
setuptools                49.4.0                   py37_0  
shapely                   1.6.4.post1              pypi_0    pypi
six                       1.15.0                   pypi_0    pypi
sqlite                    3.32.3               h62c20be_0  
tensorboard               2.3.0                    pypi_0    pypi
tensorboard-plugin-wit    1.7.0                    pypi_0    pypi
threadpoolctl             2.1.0                    pypi_0    pypi
tk                        8.6.10               hbc83047_0  
topk                      1.0                      pypi_0    pypi
torch                     1.6.0                    pypi_0    pypi
torchvision               0.7.0                    pypi_0    pypi
urllib3                   1.25.10                  pypi_0    pypi
werkzeug                  1.0.1                    pypi_0    pypi
wheel                     0.34.2                   py37_0  
xz                        5.2.5                h7b6447c_0  
zipp                      3.1.0                    pypi_0    pypi
zlib                      1.2.11               h7b6447c_3  

[qinghezeng]

I found conda install -c anaconda pixman worked with one of my conda environments.

So I would suggest to try with it first. If it doesn't work, then try to replace the files libpixman-1.so*.

[ptschandl]

(Re)installing with conda never worked for me, so I got back to a solution I created a while ago for the same issue within QuPath. Some of you may find this solution (i.e. patching pixman oneself manually) helpful:

https://forum.image.sc/t/change-image-provider-after-import/42502/4

In case you think about using the script: Read / alter to your needs, and definitely use at your own risk! You can also find the script as a gist here: https://gist.github.com/ptschandl/cd72cf279ba83b2b3178d9b32f034c15

[dkoen]

I tried running

conda install -c anaconda pixman 

which installs 0.38.0

and I tried running

conda install -c anaconda pixman=0.40.0

which results in

Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                                       
                                                                                                                                                                                             
UnsatisfiableError: The following specifications were found to be incompatible with a past                                                                                                   
explicit spec that is not an explicit spec in this operation (pixman):

  - pixman=0.40.0

The following specifications were found to be incompatible with each other:



Package pixman conflicts for:
gdk-pixbuf==2.36.9=1 -> gobject-introspection -> cairo[version='>=1.14.12,<2.0a0'] -> pixman[version='>=0.34.0,<1.0a0|>=0.38.0,<0.39.0a0']
pango==1.42.4 -> pixman[version='>=0.34.0,<1.0a0']
pango==1.42.4 -> cairo[version='>=1.14.12,<2.0a0'] -> pixman[version='>=0.38.0,<0.39.0a0|>=0.40.0,<1.0a0']
cairo==1.16.0 -> pixman[version='>=0.38.0,<0.39.0a0|>=0.40.0,<1.0a0']
librsvg==2.46.2 -> cairo[version='>=1.16.0,<1.17.0a0'] -> pixman[version='>=0.38.0,<0.39.0a0']
harfbuzz==2.4.0 -> cairo[version='>=1.14.12,<2.0a0'] -> pixman[version='>=0.34.0,<1.0a0|>=0.38.0,<0.39.0a0|>=0.40.0,<1.0a0']
gobject-introspection==1.56.1=py37hbc4ca2d_2 -> cairo[version='>=1.14.12,<2.0a0'] -> pixman[version='>=0.34.0,<1.0a0|>=0.38.0,<0.39.0a0|>=0.40.0,<1.0a0']

It seems cairo is the issue and I notice it's not in the conda list posted above

Here's mine:

# Name                    Version                   Build  Channel
2to3                      1.0                      pypi_0    pypi
_libgcc_mutex             0.1                        main  
_pytorch_select           0.1                       cpu_0  
_tflow_select             2.3.0                       mkl  
absl-py                   0.9.0                    py37_0    conda-forge
asciitree                 0.3.3                    pypi_0    pypi
asgiref                   2.3.2                    pypi_0    pypi
asn1crypto                1.2.0                    pypi_0    pypi
astor                     0.8.0                    py37_0  
async-timeout             3.0.1                    pypi_0    pypi
atomicwrites              1.3.0                    pypi_0    pypi
attrs                     19.3.0                     py_0    conda-forge
autobahn                  19.5.1                   pypi_0    pypi
automat                   0.8.0                    pypi_0    pypi
backcall                  0.1.0                    py37_0  
blas                      1.0                         mkl  
bleach                    3.1.0                    pypi_0    pypi
c-ares                    1.15.0            h7b6447c_1001  
ca-certificates           2020.10.14                    0    anaconda
cairo                     1.16.0            h18b612c_1001    conda-forge
certifi                   2020.6.20                py37_0    anaconda
cffi                      1.14.0           py37h2e261b9_0  
channels                  2.1.7                    pypi_0    pypi
click                     7.0                      pypi_0    pypi
codacy-coverage           1.3.11                   pypi_0    pypi
constantly                15.1.0                   pypi_0    pypi
coverage                  4.5.4                    pypi_0    pypi
cryptography              2.3.1                    pypi_0    pypi
cudatoolkit               10.1.243             h6bb024c_0  
cycler                    0.10.0                   py37_0  
cython                    0.29.15          py37he6710b0_0  
daphne                    2.2.5                    pypi_0    pypi
dbus                      1.13.12              h746ee38_0  
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
django                    2.2.7                    pypi_0    pypi
djangorestframework       3.9.4                    pypi_0    pypi
entrypoints               0.3                      py37_0  
expat                     2.2.6                he6710b0_0  
fasteners                 0.15                     pypi_0    pypi
filelock                  3.0.12                   pypi_0    pypi
flask                     1.0.2                    pypi_0    pypi
fontconfig                2.13.1            he4413a7_1000    conda-forge
freetype                  2.9.1                h8a8886c_1  
fribidi                   1.0.9                h7b6447c_0  
future                    0.18.2                   pypi_0    pypi
gast                      0.3.3                      py_0    conda-forge
gdk-pixbuf                2.36.9                        1    conda-forge
glib                      2.63.1               h5a9c865_0  
gmp                       6.1.2                h6c8ec71_1  
gobject-introspection     1.56.1           py37hbc4ca2d_2  
google-pasta              0.2.0                      py_0  
graphite2                 1.3.13               h23475e2_0  
grpcio                    1.27.2           py37hf8bcb03_0  
gst-plugins-base          1.14.0               hbbd80ab_1  
gstreamer                 1.14.0               hb453b48_1  
h5py                      2.10.0          nompi_py37h513d04c_102    conda-forge
harfbuzz                  2.4.0                hca77d97_0  
hdf5                      1.10.5          nompi_h3c11f04_1104    conda-forge
hyperlink                 19.0.0                   pypi_0    pypi
icu                       58.2                 h9c2bf20_1  
idna                      2.8                      pypi_0    pypi
imagecodecs               2020.2.18                pypi_0    pypi
imageio                   2.6.1                    pypi_0    pypi
importlib_metadata        1.5.0                    py37_0    conda-forge
incremental               17.5.0                   pypi_0    pypi
intel-openmp              2019.4                      243  
intervaltree              3.0.2                    pypi_0    pypi
ipykernel                 5.1.4            py37h39e3cac_0  
ipython                   7.13.0           py37h5ca1d4c_0    conda-forge
ipython_genutils          0.2.0                    py37_0  
itsdangerous              1.1.0                    pypi_0    pypi
jedi                      0.16.0                   py37_1  
jinja2                    2.11.1                     py_0    conda-forge
joblib                    0.14.0                   pypi_0    pypi
jpeg                      9b                   h024ee3a_2  
jsonfield2                3.0.3                    pypi_0    pypi
jsonschema                2.6.0                    pypi_0    pypi
jupyter_client            6.1.0                      py_0    conda-forge
jupyter_core              4.6.1                    py37_0    conda-forge
keras-applications        1.0.8                      py_0  
keras-preprocessing       1.1.0                      py_1  
kiwisolver                1.1.0            py37he6710b0_0  
ld_impl_linux-64          2.33.1               h53a641e_7    conda-forge
libblas                   3.8.0                    14_mkl    conda-forge
libcroco                  0.6.13               h8d621e5_0    conda-forge
libedit                   3.1.20181209         hc058e9b_0  
libffi                    3.2.1                hd88cf55_4  
libgcc                    7.2.0                h69d50b8_2  
libgcc-ng                 9.1.0                hdf63c60_0  
libgfortran-ng            7.3.0                hdf63c60_0  
libiconv                  1.15                 h63c8f33_5  
liblapack                 3.8.0                    14_mkl    conda-forge
libpng                    1.6.37               hbc83047_0  
libprotobuf               3.11.4               hd408876_0  
librsvg                   2.46.2               h33a7fed_1    conda-forge
libsodium                 1.0.16               h1bed415_0  
libstdcxx-ng              9.1.0                hdf63c60_0  
libtiff                   4.1.0                h2733197_0  
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13                 h1bed415_1  
libxml2                   2.9.9                hea5a465_1  
lmdb                      0.98                     pypi_0    pypi
lxml                      4.2.1                    pypi_0    pypi
lz4                       2.2.1                    pypi_0    pypi
markdown                  3.1.1                    py37_0  
markupsafe                1.1.1            py37h7b6447c_0  
matplotlib                3.1.1            py37h5429711_0  
mistune                   0.8.4            py37h7b6447c_0  
mkl                       2019.4                      243  
mkl-service               2.3.0            py37he904b0f_0  
mkl_fft                   1.0.15           py37ha843d7b_0  
mkl_random                1.1.0            py37hd6b4f25_0  
monotonic                 1.5                      pypi_0    pypi
more-itertools            8.8.0                    pypi_0    pypi
mypy-extensions           0.4.3                    pypi_0    pypi
nbconvert                 5.6.1                    py37_0    conda-forge
nbformat                  5.0.4                      py_0    conda-forge
ncurses                   6.2                  he6710b0_0  
ndg-httpsclient           0.5.0                    pypi_0    pypi
networkx                  2.4                      pypi_0    pypi
ninja                     1.9.0            py37hfd86e86_0  
notebook                  6.0.1                    py37_0    conda-forge
numcodecs                 0.6.4                    pypi_0    pypi
numpy                     1.18.1           py37h4f9e942_0  
numpy-base                1.18.1           py37hde5b4d6_1  
olefile                   0.46                     py37_0  
opencv-python             4.1.1.26                 pypi_0    pypi
openslide-python          1.1.1                    pypi_0    pypi
openslides                3.0                      pypi_0    pypi
openssl                   1.1.1h               h7b6447c_0    anaconda
packaging                 19.2                     pypi_0    pypi
pandas                    0.25.3                   pypi_0    pypi
pandoc                    2.2.3.2                       0  
pandocfilters             1.4.2                    py37_1  
pango                     1.42.4               h7062337_3    conda-forge
parso                     0.6.2                      py_0    conda-forge
pcre                      8.43                 he6710b0_0  
pexpect                   4.8.0                    py37_0    conda-forge
pickleshare               0.7.5                    py37_0  
pillow                    7.0.0            py37hb39fc2d_0  
pip                       20.0.2                   py37_1    conda-forge
pixman                    0.38.0               h7b6447c_0    anaconda
pkgconfig                 1.5.1                    pypi_0    pypi
pluggy                    0.13.1                   pypi_0    pypi
progressbar2              3.43.1                   pypi_0    pypi
prometheus_client         0.7.1                      py_0    conda-forge
prompt-toolkit            3.0.4                      py_0    conda-forge
prompt_toolkit            3.0.4                         0    conda-forge
protobuf                  3.10.0                   pypi_0    pypi
ptyprocess                0.6.0                    py37_0    conda-forge
py                        1.8.0                    pypi_0    pypi
pyasn1                    0.4.3                    pypi_0    pypi
pycparser                 2.20                       py_0    conda-forge
pyflann                   1.6.14                   pypi_0    pypi
pygments                  2.6.1                      py_0    conda-forge
pyhamcrest                1.9.0                    pypi_0    pypi
pyopenssl                 18.0.0                   pypi_0    pypi
pyparsing                 2.4.6                      py_0    conda-forge
pypdf2                    1.26.0                   pypi_0    pypi
pyqt                      5.9.2            py37h05f1152_2  
pyrsistent                0.15.7           py37h7b6447c_0  
pytest                    4.6.2                    pypi_0    pypi
pytest-cov                2.7.1                    pypi_0    pypi
python                    3.7.7           hcf32534_0_cpython  
python-dateutil           2.8.1                      py_0    conda-forge
python-spams              2.6.1           py37h55324e4_1204    conda-forge
python-utils              2.3.0                    pypi_0    pypi
python_abi                3.7                     2_cp37m    conda-forge
pytorch                   1.3.1           cpu_py37h62f834f_0  
pytz                      2019.3                     py_0    conda-forge
pywavelets                1.1.1                    pypi_0    pypi
pyyaml                    3.13                     pypi_0    pypi
pyzmq                     18.1.1           py37he6710b0_0  
qt                        5.9.7                h5867ecd_1  
readline                  8.0                  h7b6447c_0  
requests                  2.22.0                   pypi_0    pypi
requests-mock             1.5.2                    pypi_0    pypi
roman                     3.1                      pypi_0    pypi
scikit-image              0.16.2                   pypi_0    pypi
scikit-learn              0.22.1                   pypi_0    pypi
scipy                     1.4.1            py37h0b6359f_0  
seaborn                   0.9.0                    pypi_0    pypi
send2trash                1.5.0                    py37_0  
setuptools                41.6.0                   pypi_0    pypi
sip                       4.19.8           py37hf484d3e_0  
six                       1.14.0                   py37_0    conda-forge
sklearn                   0.0                      pypi_0    pypi
sortedcontainers          2.1.0                    pypi_0    pypi
sqlite                    3.31.1               h7b6447c_0  
sqlparse                  0.3.0                    pypi_0    pypi
tensorboard               1.14.0           py37hf484d3e_0  
tensorboardx              1.9                      pypi_0    pypi
tensorflow                1.14.0          mkl_py37h45c423b_0  
tensorflow-base           1.14.0          mkl_py37h7ce6ba3_0  
tensorflow-estimator      1.14.0                     py_0  
termcolor                 1.1.0                    py37_1  
terminado                 0.8.3                    py37_0    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tifffile                  2020.2.16                pypi_0    pypi
tk                        8.6.8                hbc83047_0  
toml                      0.10.0                   pypi_0    pypi
torchsummary              1.5.1                    pypi_0    pypi
torchvision               0.1.8                    pypi_0    pypi
tornado                   6.0.4            py37h7b6447c_1  
tox                       3.13.2                   pypi_0    pypi
tqdm                      4.37.0                   pypi_0    pypi
traitlets                 4.3.3                    py37_0    conda-forge
twisted                   19.7.0                   pypi_0    pypi
txaio                     18.8.1                   pypi_0    pypi
typing-extensions         3.7.4.1                  pypi_0    pypi
urllib3                   1.25.7                   pypi_0    pypi
virtualenv                16.7.7                   pypi_0    pypi
wcwidth                   0.1.8                      py_0    conda-forge
webencodings              0.5.1                    py37_1  
websockets                8.1                      pypi_0    pypi
werkzeug                  1.0.0                      py_0    conda-forge
wheel                     0.34.2                   py37_0    conda-forge
wrapt                     1.12.1           py37h7b6447c_1  
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.9                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h27cfd23_1007  
xz                        5.2.4                h14c3975_4  
zarr                      2.3.2                    pypi_0    pypi
zeromq                    4.3.1                he6710b0_3  
zipp                      2.2.0                      py_0    conda-forge
zlib                      1.2.11               h7b6447c_3  
zope-interface            4.6.0                    pypi_0    pypi
zstd                      1.3.7                h0b5b093_0  

[dkoen]

The following worked for me and two of my peers:

conda uninstall cairo 
conda install -c anaconda pixman=0.40.0
conda install cairo