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Add BIA accession number
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iimog committed Sep 24, 2024
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Expand Up @@ -14,7 +14,7 @@ This repository is archived at Zenodo [![DOI](https://zenodo.org/badge/DOI/10.52

## Data

Raw data is archived independently in the [BioImage Archive (BIA)](https://www.ebi.ac.uk/bioimage-archive/) with accession number **TODO**.
Raw data is archived independently in the [BioImage Archive (BIA)](https://www.ebi.ac.uk/bioimage-archive/) with accession number [S-BIAD1376](https://www.ebi.ac.uk/biostudies/studies/S-BIAD1376) (under embargo until publication).
In order to reproduce our analyses, download the raw data from BIA and put them into the `data/raw` folder.

Image data, acquired on the Leica DMI8 were maximum intensity projected along the z-axis and [instant computational clearing (ICC)](https://www.leica-microsystems.com/science-lab/life-science/an-introduction-to-computational-clearing/) was applied using Leica software. These images, with associated metadata consist the raw data of our analysis. Only for one dataset (2nt), the images without ICC were used for cell segmentation. Except for these non-ICC images, all datasets were convertet to [spacetx format](https://spacetx-starfish.readthedocs.io/en/latest/help_and_reference/spacetx-format/SpaceTxFormat/index.html) for further analysis.
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