<< Single Cell Portal Now Accepts AnnData Files to Power Visualizations More info

May 23, 2023

Image from AnnData documentation

Sharing data is a crucial step in the lifecycle of a research project. But in spite of its value, this step can be time-consuming, particularly when you have to re-format your data before sharing it to an online repository like Single Cell Portal. 

To reduce this burden, we’ve updated the file types that we accept for SCP studies. You can now create a Single Cell Portal study by uploading an .h5ad file containing an AnnData object. This should speed up the data contribution process by bridging the gap between the files that you work with when analyzing your data, and the files that you ultimately share with the research community. In addition, uploading AnnData to SCP will make it easier for other researchers to incorporate your data into their own analyses. While this change most directly impacts researchers who work in Scanpy, we hope that this will also benefit Seurat users who leverage existing conversion tools


How does this work? Once you’ve created a study on SCP, you’ll see two options for uploading your data:

The “classic” approach is the upload process that we’ve always supported – separate files for metadata, cluster coordinates, processed counts, and raw counts. You can read more about this classic data format here

The “AnnData” approach allows you to upload all of these data objects in a single AnnData (.h5ad) file. Right now, you can only upload a single AnnData object per study. We might expand this in the future, so if you want to include multiple AnnData objects in your study please let us know! 


This feature is still in beta mode, and your feedback will help us make it better. Fill out this 2-minute survey to share your thoughts on how we could improve SCP’s data upload process. You can also email us at scp-support@broadinstitute.zendesk.com.

Sharing your data is important for furthering single-cell science, and we hope that being able to upload AnnData files will lower the barriers for many researchers to contribute and analyze data with Single Cell Portal.