Guides

Detailed guides for getting the most out of Find Nuclei Viewer.

Opening Data

Local Files: Drag and drop OME-ZARR data from your disk
Remote URLs: Stream data from public OME-ZARR servers
Data Server: Host your own on-site ZARR server with Docker
Authenticated Sources: Open private ZARR data via Bearer tokens or AWS SigV4 (STS-scoped S3 access)
HCS Plates: Navigate high-content screening plate data

Viewing and Display

Channels: Pick colors, adjust contrast, auto-contrast, gamma, RGB/BW/INV display modes
Z-Projection: Flatten a Z-stack into one image with maximum, mean or minimum intensity

Segmentation and Analysis

Labels: Load segmentation masks, control display, add metadata, organise by source or key-value
Analytics & Phenotyping: Load CSVs, color by column, filter, and build named cell populations
Annotations: Draw, select, bulk-edit, and classify regions of interest
Annotation Templates: Create reusable template presets for color + class + keyboard shortcut

Sharing Views: Share your exact view with a URL
Embedding in Publications: Add an interactive viewer to any web page with two lines of HTML

Reference

Sample Data and Credits: Where the images in these guides come from, and how to cite them
Analytics Data Format: Publish measurements and masks so the viewer loads them from one URL