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A quick note to mention that @d33bs and I needed to perform two hotfixes of cytominer-database versions (v0.3.5) to accommodate pycytominer upload to conda-forge. You can see the change in #134
[Da…
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Hi! I am newly working on high content screening and I would like to use cytominer to analyse my data. But I have some issues following your pipeline. I have create my database with information about …
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@hkhawar and I were troubleshooting cytominer install. It was failing originally because of the issues described in #131 - we are trying to install in a conda environment, but are getting some errors.
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In working through #437 via #439 I noticed that collate has `collate` has much lower test coverage than other components within pycytominer. We could increase this coverage with some further tests, po…
d33bs updated
1 month ago
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In the readme front page the link for the most recent cytominer-eval installation is given as
`pip install git+git://github.com/cytomining/cytominer-eval@f7f5b293da54d870e8ba86bacf7dbc874bb79565`
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FloHu updated
3 years ago
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- [x] cytominer_ami.json: update `ami_name` (latest Ubuntu) and related items in `builders`
- [x] docker.sh: update to latest instructions
- [x] efs.sh: nothing
- [x] init.sh: nothing
- [ ] pyt…
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As currently defined in [aggregate.py](https://github.com/cytomining/pycytominer/blob/ac3ef680c1f4625aa1e8452b431afb5af8bcdd41/pycytominer/aggregate.py), the class `AggregateProfiles()` works using SQ…
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Once we merge cytomining/pycytominer#160, we might decide to explicitly specify an optional `cytominer-database` dependency, using a solution as recommended by @bethac07.
See https://github.com/cyt…
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At present, we have only cytominer.
Here are others I could think of
- [scanpy](https://icb-scanpy.readthedocs-hosted.com/en/stable/_)
- [PurifyR](https://github.com/womta/PurifyR)
We now als…
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Currently `cytominer_transport/_generator.py` combines objects based on "ImageNumber" and "ObjectNumber".
Instead, we should consider combining objects by their appropriate "Parent_{compartment}" a…