From 58f3cbfb09b8b2e77badab7eec9ebb70fd73edde Mon Sep 17 00:00:00 2001 From: Constantin Pape Date: Sun, 2 Apr 2023 20:41:22 +0200 Subject: [PATCH] Describe table formats WIP --- specs/template_source.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/specs/template_source.md b/specs/template_source.md index 57eee05..7948ba6 100644 --- a/specs/template_source.md +++ b/specs/template_source.md @@ -22,7 +22,7 @@ Similarly, data stored in `ome.zarr` must only contain a single channel, and the ### Table Data MoBIE supports tables associated with segmentations, where each row corresponds to properties of an object in the segmentation. -The tables should be stored as tab separated values `.tsv` files; they may also be stored as comma separated values (`.csv`). +The tables should be stored as tab separated values `.tsv` files; they may also be stored as comma separated values (`.csv`). This section describes the default MoBIE table formats; we support more formats for compatibility with other analysis software, see [the table formats section](#table-formats). The default segmentation table (which must be stored as `default.tsv` in the corresponding table folder, see also [dataset specification](#dataset)) must contain the columns `label_id`, `anchor_x`, `anchor_y`, `anchor_z`, `bb_min_x`, `bb_min_y`, `bb_min_z` and `bb_min_x`, `bb_min_y`, `bb_min_z`. For two-dimension data the columns `anchor_z`, `bb_min_z` and `bb_max_z` must be omitted. The `anchor` columns specify a reference point for the object corresponding to this row. It will be centered @@ -53,6 +53,15 @@ Data for a spot source is defined by a table. This table must contain the column Region tables also have an associated table. It is described in further detail [here](#view-source-annotations) +#### Table Formats + +- MoBIE segmentation table format: lorem ipsum + - `label_id`, `anchor_x,y,z`, `bb_min_x,y,z`, `bb_max_x,y,z`, `timepoint` +- scikit-image table format: lorem ipsum regionprops + - `label`, `centroid-0,1,2`, bbox-0,1,2,3,4,5`, `frame` +- MorphoLibJ: lorem ipsum + - `Label`, `Centroid.X,Y,Z`, `Box.X,Y,Z.Min`, `Box.X,Y,Z.Max`, `Timepoint` + ### Source Metadata