Add outline for bioimage format skew project - #1
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gwaybio
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gwaybio
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Comments relating to clarity - feel free to ignore at this time, if they are only slowing you down.
| # tesserift | ||
| Measure how bioimaging storage layouts shape performance, analysis, and biological discovery. | ||
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| Bioimaging data can follow a format specification and still perform poorly. |
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i recommend adding a bit more specificity to what you mean by "format specification". Also, what do you mean by "perform" and "poorly"? Perform what? Poorly measured how?
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| Bioimaging data can follow a format specification and still perform poorly. | ||
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| We will study around **six public datasets from three sources**, with two datasets from each source: |
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I'm wondering how you decided six datasets - is there a reason not to scan through every dataset from these three sources?
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| We will study around **six public datasets from three sources**, with two datasets from each source: | ||
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| * **Image Data Resource (IDR):** established OME bioimaging datasets with different image shapes and workloads. |
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Consider defining OME before first use.
Also, what is an "image shape" and what is an "image workload"?
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| * **Image Data Resource (IDR):** established OME bioimaging datasets with different image shapes and workloads. | ||
| * **SSBD:** multidimensional OME-Zarr data, including 3D and time-series images. | ||
| * **Cell Painting Gallery / JUMP:** large-scale imaging data with associated metadata and feature tables. |
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| * **Cell Painting Gallery / JUMP:** large-scale imaging data with associated metadata and feature tables. | |
| * **Cell Painting Gallery:** large-scale imaging data from the Cell Painting assay (e.g., JUMP) with associated metadata and morphology feature tables. |
| * **SSBD:** multidimensional OME-Zarr data, including 3D and time-series images. | ||
| * **Cell Painting Gallery / JUMP:** large-scale imaging data with associated metadata and feature tables. | ||
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| Two datasets from each source will help us measure variation both **within** and **between** public data services. |
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Two is not sufficient to measure these things - how tough would it be to measure all datasets? (i imagine what we're measuring will answer this question!)
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Adds an outline for a project and resulting paper which helps describe skew in bioimage formats along with how this impacts science.