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SenNet Portal

The SenNet Portal tab lets you discover and download SenNet datasets directly from SenoQuant.

It is designed for antibody-based imaging datasets and only allows downloads for files that match SenoQuant-supported image extensions.

Prerequisites

  • globus-cli (which provides globus) is installed automatically with SenoQuant dependencies.
  • atlas-consortia-clt (which provides sennet-clt) is installed automatically with SenoQuant dependencies.
  • Install and configure Globus Connect Personal (GCP) for local downloads.
  • Use the Login button in the Connection section to authenticate with Globus.
  • (Optional) If you need non-public datasets, provide a bearer token in the tab.

Connection panel

The Connection section includes runtime checks for Globus tools:

  • Globus status and Login/Logout controls for CLI authentication.
  • GCP status row for local endpoint availability.
  • Install Globus Connect Personal button when GCP is not detected.
  • Check again button to refresh status after installing/configuring GCP.

If your environment is behind a corporate firewall, GCP may require a Setup Key. See the official Globus instructions:

Workflow

  1. Open SenNet Portal.

  2. Choose dataset filters:

    • Dataset type (or keep Any antibody-based imaging).
    • Status (default Published).
    • Max results.

  3. Click Find datasets.

  4. Review compatible datasets in the table:

    • Only antibody-imaging datasets are included.
    • Only datasets with at least one supported file extension are shown.
    • The table columns are: SenNet ID, Type, Source type, Organ, Age, Status, Access, and Files.

  5. Optionally use the filter row under the table headers:

    • Filters are available for all metadata columns (SenNet ID, Type, Source type, Organ, Age, Status, Access, Files).
    • Filters hide non-matching rows and exclude them from download.

  6. Select rows to download:

    • Select all / Clear all apply only to rows currently visible in the table.
    • Clear filters resets all filters and shows all rows again.

  7. Set a Destination folder.

  8. Click Download selected.

Supported extensions

The portal filters files dynamically using the extensions supported by the SenoQuant reader (via BioIO plugin registration).

Dataset table columns and filters

  • Age column:

    • Age is a best-effort normalized sample age value from SenNet metadata.
    • Age is shown as a display string such as 30 years or 18 months.
    • For Mouse sources, age is displayed in months; for other sources, age is displayed in years.
    • If age cannot be derived from available metadata, Age is shown as Unknown.

  • Age filter:

    • The Age filter uses Min and Max numeric fields in the filter row under the Age header.
    • Rows match only when their numeric age value is within the specified bounds.
    • Rows with Unknown (non-numeric) age are excluded whenever a Min or Max age filter is active.
    • Non-numeric Min/Max inputs are ignored.

  • Filter selection behavior:

    • When any filter is active, matching rows remain visible and selected, while non-matching rows are hidden and unchecked.
    • Select all / Clear all affect only currently visible rows.
    • Clear filters resets all categorical and age-range filters.

Notes

  • File compatibility is resolved from SenNet Search API param-search/files.
  • Transfers use SenNet CLI manifest mode internally.
  • If your selected destination is outside your home directory, SenoQuant stages the transfer and then moves files into your chosen folder.
  • A sennet_dataset_metadata.json is written in each dataset output folder, including the full Entity API payload for that dataset.