Creating an Image Preview

How to run a Pennsieve Analysis Workflow so an image becomes viewable on the Orthogonal Viewer — Pennsieve's Neuroglancer-based 2D/3D viewer.

Nifti Asset Processor.nii · .nii.gz
Ome-Tiff Assets Processor.ome.tiff
Zipped Zarr Assets Processorzarr.zip

Before you start

You'll need the following access in place. If anything is missing, contact Pennsieve support.

Access to the compute node — SPARC - Compute Node 2. It must be shared with you.
Permissions on the dataset that contains the files you want to convert.

Walkthrough

Log in and open Analytics

Log in to Pennsieve and navigate to your workspace. In the left sidebar, click Analytics. At the top of the Analytics page, make sure you're on the Runs tab.

Initiate a new workflow

In the top right of the Runs tab, click Initiate Workflow.

Select the processor

Use the search bar to find the processor that matches your file type:

NIfTI files → Nifti Assets Processor
OME-TIFF files → Ome Tiff Asset Processor
Zipped zarr files → Zipped Zarr Asset Processor

Select the compute node

Select SPARC - Compute Node 2 as the compute node, then click Next.

Note If you don't see SPARC - Compute Node 2, you don't have access yet. Reach out to Pennsieve support to request it.

Select the dataset

Search for and select the dataset that contains the files you want to process. Click Next.

Open the configure run page

Click Configure to open the configuration page for the run.

Choose your source files

On the configure run page, click the Data Source box on the right side. A file browser will pop up. Navigate to the NIfTI or OME-TIFF file you want to convert.

Important You can only select one file per workflow run.

When finished selecting, click Done.

Configure the processor

Click the processor box (the middle box) on the configure run page. On the right panel, set the CPU and Memory to their highest available settings.

Configure the output asset

There are two Pennsieve Package Asset boxes for each workflow — one creates an explorable preview of the image, the other creates a small thumbnail for the Gallery. Set the ASSET_TYPE on both.

Box connected to the Zarr Thumbnail Processor (left panel)

ASSET_TYPE → "thumb"

Pennsieve Package Asset configuration panel

Box underneath the first processor, on the right — titled after your image type (proccessor-unzipp, Pennsieve/processor_tiff_zarr_converter, or Pennsieve/Nifti-To-Zarr-Conversion)

ASSET_TYPE → "ome-zarr"

Execute the workflow

When everything is configured, click Execute Workflow in the top right.

That's it — the workflow is now running. Once it completes, the converted files will be available for preview within the Pennsieve platform.

Tip You can re-run a workflow with your same configuration by selecting it in Runs and clicking "Re-run with configuration" in the bottom right.

Troubleshooting

Compute node not visible

The SPARC - Compute Node must be shared with you. Contact Pennsieve support to request access.

Dataset not visible

You need permissions on the dataset containing the source files. Request access from the dataset owner.

Can't select a folder

Expected — source files must currently be selected one at a time.