add annotation naming scheme #21
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added 2 commits
October 4, 2024 11:08
kabilar
reviewed
Oct 15, 2024
| @@ -139,6 +139,20 @@ This directory contains microscopy data files [as described in detail in the BID | |||
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| In this example the data include images (`.tif`) and metadata (`.json`) from multiple brain sections. For each section there is a blockface photo (`_photo`) and a histological stain (`_stain`). Sections from Ken1 and Ken2 were either processed with a Nissl stain and imaged under brightfield microscopy (`_BF`), or processed for the fluorescent tracer Lucifer Yellow (`LY`) and imaged under darkfield microscopy (`_DF`). Additional sections from Ken2 were processed for the fluorescent tracer Fluoro-Ruby (`FR`) and imaged under darkfield microscopy (`_DF`). | |||
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| #### high-res histology annotation | |||
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Thank you, @jssyq. Do we also want to have a sidecar <matches>.tsv file or top-level dseg.tsv that specifies how the integer values of the segmentations map to custom labels? For example, in our case the labels could correspond to the different injection sites (or however we name the Segments in Webknossos).
kabilar
reviewed
Oct 15, 2024
| dataset name + _suffix | ||
| when annotating discrete segmentations, use _dseg as the suffix. | ||
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| When there are multiple annotators working on the same dataset, each annotation file is distinguish by adding a _desc-[label] entity before the suffix, where [label] is replaced by the annotator's initials. |
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Suggested change
| When there are multiple annotators working on the same dataset, each annotation file is distinguish by adding a _desc-[label] entity before the suffix, where [label] is replaced by the annotator's initials. | |
| When there are multiple annotators working on the same dataset, each annotation file is distinguish by adding a `_desc-[label]` entity before the suffix, where `[label]` is replaced by the annotator's initials. |
kabilar
reviewed
Oct 15, 2024
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| When there are multiple annotators working on the same dataset, each annotation file is distinguish by adding a _desc-[label] entity before the suffix, where [label] is replaced by the annotator's initials. | ||
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| For example, an annotator with an initial JS would name the annotation file as sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg |
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Suggested change
| For example, an annotator with an initial JS would name the annotation file as sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg | |
| For example, an annotator with an initial JS would name the annotation file as follows: | |
| `sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg.ome.zarr` |
kabilar
reviewed
Oct 15, 2024
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| All annotation files use the following naming scheme: | ||
| dataset name + _suffix | ||
| when annotating discrete segmentations, use _dseg as the suffix. |
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Suggested change
| All annotation files use the following naming scheme: | |
| dataset name + _suffix | |
| when annotating discrete segmentations, use _dseg as the suffix. | |
| All annotation files use the following naming scheme: | |
| `<dataset-name>_suffix.ome.zarr` | |
| When annotating discrete segmentations, use `_dseg` as the suffix (see the [BIDS spec on discrete segmentations](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#discrete-segmentations)). |
kabilar
reviewed
Oct 15, 2024
Comment on lines
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+148
| All annotation files use the following naming scheme: | ||
| dataset name + _suffix | ||
| when annotating discrete segmentations, use _dseg as the suffix. |
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Will we know ahead of time which datasets will have multiple annotators? If not, perhaps we should always add the annotator's initials to the file name?
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