Overview

Celery is a tool to annotate spatial transcriptomic data in the web. It allows for multiple users to annotate or view the same sample, and all progress is automatically synced with a database. Data from Visium and Pyseq 4i are supported. There exists partial support for original ST.

Tabs

Project Summaries

View the annotation status for each tissue in your assigned projects.

Curated Annotations

Perform tissue annotations by hand using the specified anatomical regions. You may add, edit, or delete existing annotations for samples which are not marked as "completed". Visium annotations from Loupe Browser may be imported as a .csv and the current annotations can also be exported as a .csv.

Computed Annotations

W.I.P - View annotations predicted my ML models. Predicted annotations in this tab may be copied over to "Curated Annotations"

Gene Expression

Select genes or calculated QC metrics to view for Visium-style data. You may view multiple genes/features simultaneously and selected spots will carry over to the "Curated Annotations" tab.

Data Upload

Registered users may upload projects and samples to the database via the command line tool found in this repository. Since it is not possible to authenticate a user from the command line, a user token must be passed as arguments to the upload scripts. To get your temporary user token, click the "Get Token" button found below.