πŸ“‹ Documentation Version Notice

You're reading the documentation for a development version (master). For the latest released version, please have a look at v1.7.

Getting Started

This guide follows the tasks most people perform in OMERO.biomero: adding data, running a workflow, monitoring progress, and finding results.

Before You Start

Open OMERO.web at the address provided by your system administrator and select the BIOMERO panel from the top navigation bar. The active OMERO group matters: it controls which remote-storage folder you can browse and where imported or analyzed data is placed.

Important

Follow the confirmation shown after submitting an analysis. If it says the workflow runs in the background, detached mode is active and you may close the tab or log out. If it warns you to keep the session active, the workflow is running inline and logging out may prevent it from finishing. Do not assume that detached analysis also applies to a browser upload that is still transferring data.

Tip

πŸŽ₯ Live demonstration Β· 5:39: See NL-BIOMERO in practice during a real session. The current interface has since gained the web uploader, Bilayers workflows, and some updated dialogs.

Interface at a Glance

The available tabs depend on the features enabled by your administrator.

Import
Import Images

Browse the remote-storage folder mapped to your active OMERO group and start an in-place import.

Upload Images (when enabled)

Upload supported individual files from your computer. After the upload completes, the files enter the same asynchronous importer route. See the Resumable Web Uploader guide for supported files and additional details.

Monitor

Follow active and completed import orders. Each order has a UUID that can be used when locating data or asking an administrator for help.

Analyze
Image Workflows

Run workflows on selected datasets or individual images.

Plate Workflows (when configured)

Run plate-aware workflows that receive a complete plate as Zarr and preserve its well and acquisition structure.

Status

Follow queued, running, completed, and failed workflow runs. Each run has a Workflow ID (UUID) that also identifies its returned results.

How Do I Add Data Already on Remote Storage?

Use this route for files or folder-based datasets that already reside on shared storage:

  1. Select the OMERO group that should own the imported data.

  2. Open BIOMERO > Import > Import Images.

  3. Browse the folder made available to that group and select the data to import.

  4. Choose the requested destination and preprocessing options, if any, then start the import.

  5. Open Import > Monitor to follow the order and record its UUID.

The importer can optionally run a versioned preprocessing container before registering the result. The original data remains on shared storage; OMERO stores the metadata and file references needed to access it.

How Do I Add Data Directly from the Web?

Use the uploader for supported individual files on your computer:

  1. Open BIOMERO > Import > Upload Images.

  2. Select the target project or dataset shown by the interface.

  3. Add the files and start the upload. Interrupted uploads can resume.

  4. After assembly, OMERO.biomero creates an import order automatically.

  5. Follow that order under Import > Monitor.

Folder-based formats and datasets whose directory structure must be preserved should use Import Images from remote storage instead. If Upload Images is not visible, the feature has not been enabled for this deployment. See Resumable Web Uploader for the full behavior and supported-file limitations.

How Do I Run a Workflow on My Images?

  1. Make sure the input images, dataset, or plate are available in OMERO.

  2. Open BIOMERO > Analyze.

  3. Choose Image Workflows for images or datasets, or Plate Workflows for a compatible plate-aware workflow.

  4. Select the workflow and its input data.

  5. Configure the exposed parameters and output destination, then submit the run.

  6. Open Analyze > Status and record the Workflow ID.

When processing finishes, BIOMERO returns supported image and file outputs to OMERO with provenance metadata. Search for the Workflow ID in OMERO.web to find the returned results.

How Do I Get a New Workflow into BIOMERO?

You cannot install a new workflow from the normal user interface. Ask your BIOMERO administrator and provide the workflow repository, required version, expected input type, and intended use. The administrator must review, register, and initialize the pinned workflow before it becomes available.

Workflow authors can start with Adding Your Workflow to BIOMERO. Administrators should follow Adding New Workflows.

Frequently Asked Questions

I cannot find my folder on the remote disk

First confirm that the correct OMERO group is active. Each group can be mapped to a different remote-storage folder, so switching groups changes what the browser can show. If the folder is still absent, ask an administrator to check the group-folder mapping and storage permissions.

The Upload Images tab is missing

The web uploader is optional and must be enabled by an administrator. Use Import Images if the data is already on shared storage, or ask the administrator to review the Resumable Web Uploader setup.

The workflow I need is missing

It may not yet be registered or initialized, or it may appear only under Plate Workflows because of its input type. Give the workflow name and desired version to your administrator. Administrators can check Adding New Workflows.

My import or workflow is not progressing

Check Import > Monitor or Analyze > Status and copy the order or Workflow UUID. A detached analysis does not require the original OMERO session to remain active; an inline analysis does. Send the UUID and approximate start time to your administrator, since those identifiers connect the interface entry to the BIOMERO database and service logs. Administrators can review Detached BIOMERO Workflows.

Where are my workflow results?

After a successful run, search OMERO.web for the Workflow ID shown under Analyze > Status. Returned images are imported automatically and carry metadata linking them to the workflow run. If the run says it completed but no results appear, give the Workflow ID to your administrator.