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While working on `cytominer-database` data comparisons for #30 I noticed variations in how floating point numbers are treated. As an example, the number `3.5215257120407011` may be found within `.test…
d33bs updated
6 months ago
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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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A common issue that keeps surfacing involves how missing values are handled in CellProfiler, and, subsequently, in downstream image-based profiling pipelines.
There appear to be many somewhat indep…
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@jccaicedo can you clarify the metric you are now using for evaluating representations, and how you are reporting it?
IIUC you were previously using this
https://github.com/broadinstitute/DeepProf…
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The most common entrypoint to pycytominer is in the form of `sqlite` files. These files contain tables for each compartment, which themselves contain single cell morphology measurements.
Increasing…
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The purpose of this issue is to create a list. Once we settle on a list, we will close the issue and create an issue per QC item. We also need to decide where to implement this – here or in http://git…
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In the [cell health](https://github.com/broadinstitute/cell-health) project, I noticed some strange behavior with a specific plate.
The plate is `SQ00015221` coming from plate map `C-7161-01-LM6-01…
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How shall users interact with the codebase? Let's track our thoughts and decide here
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For our notes, there are two alternate paths that either replicate cytominer-database functionality or obviate its need
1. @gwaygenomics works directly with CSVs in pooled Cell Painting experiments…
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Come up with a solution for ingesting CSVs into a backend that is more scalable than SQLite.
Context: The package `cytominer-database` is a key component of image-based profiling workflows: it is a…