Pre-installed software
Check which tools and Python libraries a sandbox includes before your agent installs anything.
Every sandbox starts from the same image, so your agent can use the software on this page without an install step. Each image release pins exact package versions, and versions change when the image is updated. To see the versions in your sandbox, ask your agent to run pip list.
Base environment
| Component | Details |
|---|---|
| Operating system | Debian 12 (bookworm), x86-64 |
| Language | Python 3.12 |
Command-line tools
| Tool | Use |
|---|---|
elembio | ElemBio CLI, signed in as you. Lists, mounts, and downloads runs, executions, and storage. |
ratarmount | Mounts an archive, such as a .zarr.zip file, as a read-only directory. |
uv | Installs Python packages. |
| Shell utilities | git, curl, wget, jqzip, unzip, bzip2, xztree, file, ps, top |
Element packages
| Package | Import name | Use |
|---|---|---|
elembio-spatialdata-analysis | elembio_spatialdata_analysis | Load, quality-check, and analyze Spatial Data Objects. |
Multiomics skills direct your agent to this package for Cytos™ analysis.
Python libraries
| Category | Libraries |
|---|---|
| Spatial and single-cell data | |
| Clustering, embedding, and integration | |
| Statistics and differential expression | |
| Data frames, arrays, and storage formats | |
| Images and geometry | |
| Performance | |
| Plotting | |
| Documents and reports |
Install more packages
When a task needs a library that is not listed, your agent installs it with the install_packages tool, which runs pip in the sandbox.
- Installed packages last for the life of the sandbox. A new sandbox, or a failed resume, starts from the image again.
- Version specifiers such as
numpy==2.1.0are accepted.