Introduce workflow for element-zstack #2
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Has the example data been approved to be made public and subsequently placed in our public S3 bucket? |
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I could be mistaken, but the only GitHub Actions files we need are in the |
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
I'm following up on this internally now.
This will be updated in the next commit. |
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
This reverts commit 74330f9.
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>
| model_type="nuclei", | ||
| channels=[[0, 0]], | ||
| z_axis=0, | ||
| skip_duplicates=True, |
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| skip_duplicates=True, |
| to ensure you have `resource-manager` permissions for your account. | ||
| 2. Follow the instructions below to set up the | ||
| [intern](https://github.com/jhuapl-boss/intern) REST API locally. | ||
| + Create a new folder `.intern` in your root directory. |
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| + Create a new folder `.intern` in your root directory. | |
| + Create a new folder `.intern` in your user directory. |
| model_type="nuclei", | ||
| channels=[[0, 0]], | ||
| z_axis=0, | ||
| skip_duplicates=True, |
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| skip_duplicates=True, |
| segmentation_method="cellpose", | ||
| paramset_idx=2, | ||
| params=dict( | ||
| diameter=None, |
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Should it be 8 or None?
| diameter=None, | |
| diameter=None, |
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| @pytest.fixture(scope="session") | ||
| def volume_segmentation_task(pipeline): | ||
| volume = pipeline["volume"] |
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| volume = pipeline["volume"] | |
| volume = pipeline["volume"] | |
| key = (volume.Volume & "subject='subject1'").fetch1("KEY") |
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| @pytest.fixture(scope="session") | ||
| def volume_segmentation_task(pipeline): |
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| def volume_segmentation_task(pipeline): | |
| def volume_segmentation_param_set(pipeline): |
kabilar
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Thanks @kushalbakshi! Great work. Please add my few remaining suggestions in a subsequent pull request.
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Hi @kushalbakshi, when you have a chance, please add these remaining suggestions in a subsequent pull request. Thank you. |
3 participants
This PR sets up a workflow for
element-zstackwith the goal of allowing a user to utilize the DataJoint pipeline for processing volumetric data and automatically uploading the results to BossDB.The following list of items has been completed on this PR:
pytest results: