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Document label_image_id #104

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imagejan opened this issue Mar 23, 2023 · 3 comments
Open

Document label_image_id #104

imagejan opened this issue Mar 23, 2023 · 3 comments

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@imagejan
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The label_image_id column is added for tables including multiple sources (e.g. from a merged grid view of many segmentations), but it's not mentioned anywhere here in the documentation.

I guess it should be added at least here:

MoBIE contains three different kinds of tables:
- tables associated with a segmentation, which always contain the column **label_id**. This column represents the id (pixel value) of the corresponding segmented object. **label_id** is an integer.
- tables associated with regions (for example positions in a grid-view), which always contain the column **region_id**. This column represents the id of a region and can be an integer or string.
- tables associated with spots (e.g. gene detections in spatial transcriptomics data), which always contain the column **spot_id**. This column represents the id of a spot and is an integer.

@constantinpape
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constantinpape commented Mar 23, 2023

The label_image_id column is added for tables including multiple sources (e.g. from a merged grid view of many segmentations), but it's not mentioned anywhere here in the documentation.

This column is added automatically by the viewer, so we don't need to save it explicitly in the table on disc.

Is this still up-to-date @tischi?

@imagejan do you run into any issue if you don't provide this column?

@imagejan
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Ah, ok, so I still provide the table with each image separately? Or is there a way to provide a single table for many sources/wells?

Sorry, I'm just starting to learn how MoBIE works 🙂

@tischi
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tischi commented Mar 23, 2023

For label images you currently must provide a table for each image separately.

If you then do a grid view it will automatically join them for you, just for the viewing.

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