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More table formats #105

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Describe table formats WIP
constantinpape Apr 2, 2023
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Merge branch 'master' into table-formats
constantinpape Apr 19, 2023
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11 changes: 10 additions & 1 deletion specs/template_source.md
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Expand Up @@ -22,7 +22,7 @@ Similarly, data stored in `ome.zarr` must only contain a single channel, and the
### <a name="table"></a>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
Expand Down Expand Up @@ -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)

#### <a name="table-formats"></a>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`


### <a name="source-metadata"></a>Source Metadata

Expand Down