From c5b332275b5aaf6e7a0c2e4f9082f8d6312dfea8 Mon Sep 17 00:00:00 2001 From: Jasmine Shao <124855181+jssyq@users.noreply.github.com> Date: Tue, 29 Oct 2024 11:48:51 -0400 Subject: [PATCH] Update docs/upload.md Co-authored-by: Kabilar Gunalan --- docs/upload.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/upload.md b/docs/upload.md index 5b886e3..3060ce2 100644 --- a/docs/upload.md +++ b/docs/upload.md @@ -145,7 +145,7 @@ All annotation files use the following naming scheme: ` + _desc-[label] + _suffix.ome.zarr` where `[label]` is replaced by the annotator's initials and `_suffix` indicates the type of segmentations being annotated. Specifically, 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)). -For example, an annotator with an initial JS annotating discrete segments would name the annotation file as `sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg.ome.zarr` +For example, an annotator with an initial JS annotating discrete segments would name the annotation file as `000003_sub-MR243_sample-slice0000slice0004_stain-LY_DF_desc-JS_dseg.ome.zarr` A `.tsv` file could be included to map the IDs (integer values) of the discrete segmentations to the custom labels, where `` is replaced by the name of the annotation file. It contains a lookup table with the following columns (see the [BIDS spec on custom TSV](https://bids-specification.readthedocs.io/en/stable/derivatives/imaging.html#common-image-derived-labels)): ```