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The current implementation of sphering in pycytominer uses a constant value (`1e-6`) for the regularization parameter `epsilon`.
https://github.com/cytomining/pycytominer/blob/a5dac9e3fa3cdf61e9607…
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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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In profiling mode, if provided with images of different sizes than the specified in the config (in `config["dataset"]["images"][{"width", "height"}]`), DP will silently generate incorrect crops.
I…
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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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This issue continues work towards efforts mentioned in #214 to gain Docker-Sponsored Open Source (DSOS) sponsorship based on feedback received from Docker. This work may involve additional updates to …
d33bs updated
4 months ago
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Sometimes (~0.5% of the time by my estimation of seeing 0-10 failures per thousand CSVs checked) MeasureImageQuality in 2.2.0 doesn't actually run all the steps you ask it. This does not return an er…
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```sh
sw_vers -productVersion
# 12.6.3
conda --version
# conda 23.1.0
```
```sh
conda env create --force --file benchmark/environment.yml
```
```
Collecting package metadata (repodata.j…
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This is an optimization issue.
When running metrics such as precision-recall or enrichment, like in the demo book: https://github.com/cytomining/cytominer-eval/blob/master/demos/CellPainting_Demo.ip…
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Hi @rohban-lab et al! 👋
First of all, thank you for posting your code for your new preprint! I recently read it - congrats on the important work!
I'd like to invite you to contribute some of yo…
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In #111 - I add a method in the `cells.py` class to merge tables using predefined "linking" columns.
If there are more than the default compartments in the provided input file (e.g. single cell SQL…