scverse / scverse/spatialdata

Cannot aggregate Labels2DModel by ShapesModel

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method: aggregation 🔢 question ❓
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Description

Hi @LucaMarconato ! I got an error when I use aggregate() to aggregate a label layer by a shape layer.

Here is my code:

image

image

image

The label layer in codex_sdata was created by code below:

segmentation = iio.imread(data_dir / '3-D2_segmentation_borders.tiff')
labels = { 'labels': sd.models.Labels2DModel.parse(segmentation, dims=("y", "x")) }
sdata = sd.SpatialData(table=table, labels=labels, images=images)

In addition, following the conclusion of last Thursday's community meeting, I sent you an email with the subject 'Inquiry Regarding CODEX Data and High-Resolution Visium Image Alignment.' It contained attachments with the test data and scripts I provided. I wanted to confirm whether you received that email?

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Research direction

Start by reproducing the reported aggregate() operation using the Labels2DModel.parse(segmentation, dims=("y", "x")) setup and the label and shape layers shown in the issue. Inspect the resulting error and determine what is needed for aggregation to complete successfully; done means a Labels2DModel can be aggregated by a ShapesModel without the reported failure.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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