Update HeLa DIC Cell Segmentation (U-Net)

[bioimageiobot]

This is an automatic PR created by the @bioimageiobot regarding changes to the resource item 10.5281/zenodo.6827058.
The following version(s) will be added:

• 6827059 (version 1)

Please review the changes and make sure the new item or version(s) pass the following check list:

• Passed the BioImage.IO CI tests: static (and dynamic) validations
• The meta information for the RDF item is complete
  • The tags are complete and describe the model
  • Naming is intuitive and descriptive, example: Multi-Organ Nucleus Segmentation (StarDist 2D)
  • Authors are provided
  • Documentation is complete
    • For models, include an overview, describe how the model is trained, what is the training data, how to use the model, how to validate the results and list the references. TODO: Model documentation template.
• Approved by at least one of the BioImage.IO admin team member.

Maintainers: @esgomezm

Note: If you updated or re-uploaded another version for the current item on Zenodo, this PR won't be changed automatically. To proceed, you can do the following:

1. Block this version, but keep looking for future versions: Edit the current resource.yaml and keep the top-level status field as accepted, but change the status under the current version to blocked.
2. Accept this version and keep looking for future versions: Merge this PR for now.
3. Keep proposed version(s) (and this resource in general if it is new) as pending: Close this PR without merging.

Then wait for the CI on the main branch to complete. It should detect the new version(s) and create another PR for the new version(s).

Previous PRs of this resource: none

[netlify]

❌ Deploy Preview for collection-bioimage-io failed.

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[FynnBe]

conda env yaml:

channels: [conda-forge, defaults]
dependencies: [bioimageio.core, 'tensorflow >=1.13,<1.14']
name: '6827059'

local command:

(base) fynn@LAPTOP-BUF8ERDC:/mnt/c/Users/fbeut$ mamba create --dry-run -n test -c conda-forge bioimageio.core 'tensorflow>=1.13,<1.14'

local output

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.25.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████


Looking for: ['bioimageio.core', "tensorflow[version='>=1.13,<1.14']"]

pkgs/main/noarch                                              No change
pkgs/r/linux-64                                               No change
pkgs/main/linux-64                                            No change
pkgs/r/noarch                                                 No change
conda-forge/noarch                                   9.7MB @ 304.6kB/s 32.0s
conda-forge/linux-64                                26.0MB @ 513.1kB/s 51.5s
warning  libmamba Extracted package cache '/home/fynn/conda/pkgs/libprotobuf-3.8.0-h8b12597_0' has invalid 'repodata_record.json' file: [json.exception.type_error.302] type must be number, but is null
Transaction

  Prefix: /home/fynn/conda/envs/test

  Updating specs:

   - bioimageio.core
   - tensorflow[version='>=1.13,<1.14']


  Package                        Version  Build                   Channel                    Size
───────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
───────────────────────────────────────────────────────────────────────────────────────────────────

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  + charset-normalizer             2.1.1  pyhd8ed1ab_0            conda-forge/noarch       Cached
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  + ld_impl_linux-64              2.36.1  hea4e1c9_2              conda-forge/linux-64     Cached
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  + libblas                        3.9.0  16_linux64_openblas     conda-forge/linux-64     Cached
  + libbrotlicommon                1.0.9  h166bdaf_7              conda-forge/linux-64     Cached
  + libbrotlidec                   1.0.9  h166bdaf_7              conda-forge/linux-64     Cached
  + libbrotlienc                   1.0.9  h166bdaf_7              conda-forge/linux-64     Cached
  + libcblas                       3.9.0  16_linux64_openblas     conda-forge/linux-64     Cached
  + libcurl                       7.85.0  h2283fc2_0              conda-forge/linux-64      359kB
  + libdeflate                      1.10  h7f98852_0              conda-forge/linux-64     Cached
  + libedit                 3.1.20191231  he28a2e2_2              conda-forge/linux-64     Cached
  + libev                           4.33  h516909a_1              conda-forge/linux-64     Cached
  + libffi                         3.4.2  h7f98852_5              conda-forge/linux-64     Cached
  + libgcc-ng                     12.1.0  h8d9b700_16             conda-forge/linux-64     Cached
  + libgfortran-ng                12.1.0  h69a702a_16             conda-forge/linux-64     Cached
  + libgfortran5                  12.1.0  hdcd56e2_16             conda-forge/linux-64     Cached
  + libgomp                       12.1.0  h8d9b700_16             conda-forge/linux-64     Cached
  + liblapack                      3.9.0  16_linux64_openblas     conda-forge/linux-64     Cached
  + libnghttp2                    1.47.0  hff17c54_1              conda-forge/linux-64      844kB
  + libnsl                         2.0.0  h7f98852_0              conda-forge/linux-64     Cached
  + libopenblas                   0.3.21  pthreads_h78a6416_3     conda-forge/linux-64     Cached
  + libpng                        1.6.38  h753d276_0              conda-forge/linux-64     Cached
  + libprotobuf                    3.8.0  h8b12597_0              conda-forge/linux-64     Cached
  + libsqlite                     3.39.4  h753d276_0              conda-forge/linux-64      822kB
  + libssh2                       1.10.0  hf14f497_3              conda-forge/linux-64      239kB
  + libstdcxx-ng                  12.1.0  ha89aaad_16             conda-forge/linux-64     Cached
  + libtiff                        4.4.0  h0fcbabc_0              conda-forge/linux-64     Cached
  + libwebp-base                   1.2.4  h166bdaf_0              conda-forge/linux-64     Cached
  + libxcb                          1.13  h7f98852_1004           conda-forge/linux-64     Cached
  + libzlib                       1.2.12  h166bdaf_4              conda-forge/linux-64       66kB
  + libzopfli                      1.0.3  h9c3ff4c_0              conda-forge/linux-64     Cached
  + lz4-c                          1.9.3  h9c3ff4c_1              conda-forge/linux-64     Cached
  + markdown                       3.4.1  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + markupsafe                     2.1.1  py37h540881e_1          conda-forge/linux-64     Cached
  + marshmallow                   3.18.0  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + marshmallow-jsonschema        0.13.0  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + marshmallow-union       0.1.15.post1  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + mock                           4.0.3  py37h89c1867_3          conda-forge/linux-64       52kB
  + ncurses                          6.3  h27087fc_1              conda-forge/linux-64     Cached
  + nomkl                            1.0  h5ca1d4c_0              conda-forge/noarch          4kB
  + numexpr                        2.8.3  py37h85a3170_100        conda-forge/linux-64      137kB
  + numpy                         1.21.6  py37h976b520_0          conda-forge/linux-64     Cached
  + openjpeg                       2.5.0  h7d73246_1              conda-forge/linux-64     Cached
  + openssl                        3.0.5  h166bdaf_2              conda-forge/linux-64     Cached
  + packaging                       21.3  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + pandas                         1.3.5  py37h8c16a72_0          pkgs/main/linux-64       Cached
  + pillow                         9.2.0  py37h850a105_2          conda-forge/linux-64       47MB
  + pip                           22.2.2  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + protobuf                       3.8.0  py37he1b5a44_2          conda-forge/linux-64      696kB
  + pthread-stubs                    0.4  h36c2ea0_1001           conda-forge/linux-64     Cached
  + pycparser                       2.21  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + pygments                      2.13.0  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + pyopenssl                     22.0.0  pyhd8ed1ab_1            conda-forge/noarch        123kB
  + pyparsing                      3.0.9  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + pysocks                        1.7.1  py37h89c1867_5          conda-forge/linux-64     Cached
  + python                        3.7.12  hf930737_100_cpython    conda-forge/linux-64       60MB
  + python-dateutil                2.8.2  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + python-stdnum                   1.17  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + python_abi                       3.7  2_cp37m                 conda-forge/linux-64     Cached
  + pytz                          2022.4  pyhd8ed1ab_0            conda-forge/noarch        237kB
  + pyyaml                           6.0  py37h540881e_4          conda-forge/linux-64     Cached
  + readline                       8.1.2  h0f457ee_0              conda-forge/linux-64     Cached
  + requests                      2.28.1  pyhd8ed1ab_1            conda-forge/noarch       Cached
  + rich                          12.6.0  pyhd8ed1ab_0            conda-forge/noarch        175kB
  + ruamel.yaml                  0.17.21  py37h540881e_1          conda-forge/linux-64     Cached
  + ruamel.yaml.clib               0.2.6  py37h540881e_1          conda-forge/linux-64     Cached
  + scipy                          1.7.3  py37hf2a6cf1_0          conda-forge/linux-64     Cached
  + setuptools                    65.4.1  pyhd8ed1ab_0            conda-forge/noarch        794kB
  + shellingham                    1.5.0  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + six                           1.16.0  pyh6c4a22f_0            conda-forge/noarch       Cached
  + snappy                         1.1.9  hbd366e4_1              conda-forge/linux-64     Cached
  + sqlite                        3.39.4  h4ff8645_0              conda-forge/linux-64      807kB
  + tensorboard                   1.13.1  py37_0                  conda-forge/linux-64        3MB
  + tensorflow                    1.13.1  h5ece82f_5              conda-forge/linux-64       23kB
  + tensorflow-base               1.13.1  py37h5ece82f_5          conda-forge/linux-64       78MB
  + tensorflow-estimator          1.13.0  py_0                    pkgs/main/noarch          185kB
  + termcolor                      2.0.1  pyhd8ed1ab_1            conda-forge/noarch          9kB
  + tifffile                   2021.11.2  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + tk                            8.6.12  h27826a3_0              conda-forge/linux-64     Cached
  + tqdm                          4.64.1  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + typer                          0.6.1  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + typing-extensions              4.4.0  hd8ed1ab_0              conda-forge/noarch          9kB
  + typing_extensions              4.4.0  pyha770c72_0            conda-forge/noarch         30kB
  + urllib3                      1.26.11  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + werkzeug                       2.2.2  pyhd8ed1ab_0            conda-forge/noarch        255kB
  + wheel                         0.37.1  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + xarray                        0.20.2  pyhd8ed1ab_0            conda-forge/noarch       Cached
  + xorg-libxau                    1.0.9  h7f98852_0              conda-forge/linux-64     Cached
  + xorg-libxdmcp                  1.1.3  h7f98852_0              conda-forge/linux-64     Cached
  + xz                             5.2.6  h166bdaf_0              conda-forge/linux-64     Cached
  + yaml                           0.2.5  h7f98852_2              conda-forge/linux-64     Cached
  + zfp                            0.5.5  h9c3ff4c_8              conda-forge/linux-64     Cached
  + zipp                           3.9.0  pyhd8ed1ab_0            conda-forge/noarch         14kB
  + zlib                          1.2.12  h166bdaf_4              conda-forge/linux-64       95kB
  + zlib-ng                        2.0.6  h166bdaf_0              conda-forge/linux-64     Cached
  + zstd                           1.5.2  h6239696_4              conda-forge/linux-64     Cached

  Summary:

  Install: 143 packages

  Total download: 209MB

───────────────────────────────────────────────────────────────────────────────────────────────────

Dry run. Exiting.

DryRunExit: Dry run. Exiting.

interesting lines:

  + bioimageio.core                0.5.6  pyhd8ed1ab_0            conda-forge/noarch         55kB
  + bioimageio.spec                0.4.8  pyhd8ed1ab_0            conda-forge/noarch       Cached
  ...
  + tensorflow                    1.13.1  h5ece82f_5              conda-forge/linux-64       23kB
  + tensorflow-base               1.13.1  py37h5ece82f_5          conda-forge/linux-64       78MB  

I don't understand why mamba in the ci is not able to resolve the environment.
@constantinpape any idea?