Command Line


cirro launch [--backed] [--host HOST] [--markers [MARKERS [MARKERS ...]]] [--port PORT] [--no-open] [--spatial [SPATIAL [SPATIAL ...]]] dataset [dataset ...]

The launch command opens one or more datasets in h5ad, loom, or STAR-Fusion formats. Seurat objects can be loaded after converting to h5ad or loom formats (see vignette). Annotations and sets that are created are stored on disk in a JSON format.


cirro serve [--database DATABASE] [--db_uri DB_URI] [--email EMAIL] [--auth_client_id AUTH_CLIENT_ID] [-w WORKERS] [-t TIMEOUT] [-b BIND] [--footer FOOTER] [--header HEADER] [--upload UPLOAD]

Optional Arguments


MongoDB database connection URI (default mongodb://localhost:27017/)


MongoDB database (default cirrocumulus)


Email address that server runs as


OAuth client id


The number of worker processes


Server socket to bind. Server sockets can be any of $(HOST), $(HOST):$(PORT), fd://$(FD), or unix:$(PATH). An IP is a valid $(HOST). (default


Markdown file to customize the application footer


URL to allow users to upload files


Markdown file to customize the application header

The serve command starts the cirrocumulus server for use in a shared server environment which can handle concurrent requests from multiple users. The server can optionally enforce permissions at the dataset level, in order to securely share datasets with collaborators. Additionally, annotations and sets are created collaboratively among all users authorized to view a dataset and are stored in a database. The server can be deployed on a cloud VM, an on-premise machine, or on Google App Engine. When deployed in App Engine, the server can be configured to be use Google Cloud Firestore as a database. Please note that no datasets are available until you import a dataset into cirrocumulus.

Prepare Data

cirro prepare_data [--out OUT] [--backed] [--markers MARKERS] [--groups GROUPS] [--spatial SPATIAL] dataset

Positional Arguments


Path to dataset in h5ad, loom, or Seurat format.

Optional Arguments


Directory containing 10x visium spatial data (tissue_hires_image.png, scalefactors_json.json, and tissue_positions_list.csv) or a directory containing image.png, positions.image.csv with headers barcode, x, and y, and optionally diameter.image.txt containing spot diameter


Path to JSON file that maps name to features. For example {“a”:[“gene1”, “gene2”], “b”:[“gene3”]}


Load h5ad file in backed mode


List of groups to compute markers for (e.g. louvain)


Path to output directory

The prepare_data command is used to freeze an h5ad, loom, or Seurat file in cirrocumulus format. The cirrocumulus format allows efficient partial dataset retrieval over a network (e.g. Google or S3 bucket) using limited memory.