diff --git a/docs/upload.md b/docs/upload.md index b13d8e0..3060ce2 100644 --- a/docs/upload.md +++ b/docs/upload.md @@ -139,6 +139,25 @@ This directory contains microscopy data files [as described in detail in the BID 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`). + +#### high-res histology annotation +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 `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)): +``` +index name +1 Single Fiber +2 Light Bundle +3 Moderate Bundle +... +``` + + + ### samples.tsv This text file is [described in detail in the BIDS specification](https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files.html#samples-file). For Ken1, the `samples.tsv` would look like this: @@ -150,6 +169,7 @@ sub-Ken1 sample-slice0009 tissue sub-Ken1 sample-slice0010 tissue ``` + ## Upload your data Upload the data from your local machine to lincbrain.org: