omero-browser-qt

Reusable PyQt6 dialog for browsing and retrieving images from OMERO servers.

Features

• Login dialog with server-name history, automatic 10-minute OMERO session reuse, and runtime-only credential recall while the app stays open
• QuPath-style browser — group/owner filters, lazy-loading tree, thumbnail preview, attribute table, and name filter
• ICE pixel loading — full 5-D arrays or tile-based dask lazy loading for large / pyramidal images
• OMERO viewer — installable multi-channel viewer for 2D slices, projections, channel toggling, and playback
• 3D volume viewer — GPU-accelerated rendering via vispy with MIP, Attenuated MIP, Translucent, Average, Isosurface, Additive, and context-aware MinIP
• Interactive 3D controls — per-mode slider behavior, downsampling, smooth/nearest interpolation toggle, and free Arcball rotation
• Embeddable in any PyQt6 application

Prerequisites

omero-py requires ZeroC ICE (pre-built wheels for Python 3.10–3.12):

# Example for Python 3.11 on Windows — see docs for all platforms
pip install https://github.com/glencoesoftware/zeroc-ice-py-win-x86_64/releases/download/20240325/zeroc_ice-3.6.5-cp311-cp311-win_amd64.whl
pip install omero-py

Or via conda: conda install -c conda-forge zeroc-ice omero-py

See the Getting Started guide for all platforms.

Installation

pip install omero-browser-qt

This installs the reusable browser/dialog package and the omero_viewer launcher. On Windows, pip creates omero_viewer.exe in the environment's Scripts directory.

For full 3D viewer support:

pip install "omero-browser-qt[viewer]"

Quick start

from PyQt6.QtWidgets import QApplication
from omero_browser_qt import OmeroGateway, OmeroBrowserDialog

app = QApplication([])
gw = OmeroGateway()

for img in OmeroBrowserDialog.select_images(gateway=gw):
    print(img.getName(), img.getId())

gw.disconnect()

For structured selection with project/dataset breadcrumbs:

for ctx in OmeroBrowserDialog.select_image_contexts():
    print(ctx.breadcrumb, ctx.image.getId())

Single-select mode

By default the browser allows selecting multiple images. Pass multiselect=False to restrict the dialog to a single selection:

images = OmeroBrowserDialog.select_images(multiselect=False)
# images contains at most one ImageWrapper

contexts = OmeroBrowserDialog.select_image_contexts(multiselect=False)
# contexts contains at most one SelectedImageContext

The multiselect keyword argument is also accepted by the OmeroBrowserDialog constructor itself when embedding the dialog directly:

dlg = OmeroBrowserDialog(parent, gateway=gw, multiselect=False)
if dlg.exec() == QDialog.DialogCode.Accepted:
    image = dlg.get_selected_images()[0]

OMERO Viewer

omero_viewer

From a source checkout, you can also run:

python -m omero_browser_qt.omero_viewer

See the OMERO Viewer guide for controls and features.

The login flow silently reuses a valid OMERO session for up to ten minutes across app restarts. The password itself is not written to disk.

Documentation

Full documentation: https://cellular-imaging-amsterdam-umc.github.io/omero-browser-qt/

• Getting Started — prerequisites, install, first workflow
• User Guide — browser, pixel loading, 3D viewer
• API Reference — auto-generated from docstrings
• Examples — recipes and the OMERO Viewer

License

MIT