Life Sciences Collaborative Access Team

SynchWeb / ISPyB Guide

In this guide

Guide Overview
Select a Proposal
Add a Lab Contact
Create a Shipment
Register a Protein
Register Samples
Data Management
- Viewing Your Data
- Automated Processing
Mobile Access

Viewing Your Data

Once data collection starts, ISPyB/Synchweb gives you a real-time view of everything coming off the beamline — images, snapshots, and the metrics that go with them.

Getting to your data

You can reach data collections from the ISPyB/Synchweb home page (which shows your previous and upcoming visits) or from the Visits page (which lists all visits under the current proposal). Click into a visit to see its data collections.

Time use and visit statistics

A progress bar at the top of the visit page shows how your beamtime has been used, color-coded by activity: start-up, data collection, auto-indexing, centring, robot actions, thinking time, and time remaining. A Visit Statistics button opens a fuller dashboard — timeline graphs, a per-protein breakdown, beamline parameter changes over the visit, hourly collection rates, robot/dewar usage, and a log of any faults or callouts during the session.

Making the most of your time

Spending a lot of time in "thinking" isn't automatically a problem, but if it's adding up, talk to your Local Contact or LS-CAT staff about strategies — queuing up collections in advance is often the biggest win.

The ISPyB/Synchweb toolbar

The toolbar at the top of a visit's data view gives you quick access to:

Button	What it does
Assign Containers	Match puck positions to robot dewar positions ahead of your session.
Summary	Every data collection in the visit — sample, energy, detector distance, spacegroup, unit cell, resolution, completeness, R_meas/CC½/CC_anom. Filterable and sortable.
Autoprocessing	Which autoprocessing pipelines have run, with the option to reprocess.
Visit Status	Jumps to the visit statistics summary.
Users	Hover to see who's on the visit. Added via your LS-CAT proposal access.
Dewars	Hover to see which dewars are assigned to the visit.
Sample Changer	Visual map of pin status: grey (not loaded), red (screened only), orange (data collected, no autoprocessing), blue ring (autoprocessing not yet run), green ring (autoprocessing complete).
Reprocessing	Resubmit automated processing with different parameters — see Automated Processing.
Beamline Status	Current beamline status and webcams for the visit.

The ISPyB/Synchweb toolbar at the top of a visit's data view, showing Assign Containers, Summary, Auto Processing, Visit Stats, Users, Dewars, Sample Changer, Reprocessing, and Beamline Status buttons

The toolbar at the top of a visit's data view.

Filtering by experiment type

Buttons above the data list let you filter to a specific kind of experiment; click again to clear the filter. Available views include:

The experiment-type filter toolbar above the data list in SynchWeb, with the Screenings button highlighted

Click a filter button — like Screenings — to narrow the data list to that experiment type; click it again to clear the filter.

Data Collections

Completed collections, excluding fluorescence scans and robot loads.

X-ray Centring & Grid Scans

Grid scan previews with a diffraction heatmap (spot count or Bragg-spot count from DIALS, toggleable).

Full Collections

Complete data collections only, no auxiliary measurements.

Auto Integrated

Datasets where autoprocessing successfully integrated.

Phasing

Datasets where a phasing pipeline completed successfully.

Processing Errors

Datasets where autoprocessing failed.

Screenings

Screening datasets specifically.

Robot Actions

Sample loading events, with environment and loop images.

Sample Actions

Actions like washing or annealing performed on a sample.

Favourites

Items you've starred, for quick reference later.

Sample view

Clicking through to a sample from a data collection opens its summary: information supplied before collection, links to view all samples from the same protein, dewar and shipment context, and the option to edit sample properties (handy when preparing to reprocess). Below that you'll find every data collection, grid scan, and robot load associated with that sample, using the same experiment-type filters described above.

Beamline parameters

A left-hand panel on each data collection shows the collection settings that produced it:

Flux	Photons per second at the sample.
Ω Start / Ω Osc	Starting angle and degrees of oscillation per image.
No. Images	Total images collected.
Resolution	Obtainable resolution given the detector's position.
Wavelength / Exposure / Transmission	Collection wavelength, exposure per image, and transmission relative to beamline maximum.
Beamsize	Requested beam size (H × V, microns).
Comment	Free-text notes relevant to the sample or collection, including any centring issues.

Diffraction images and crystal photos

Click a preview image to open the interactive image viewer, which supports adjustable thresholding and full-screen viewing with optional ice-ring markers. These previews are lossy JPEGs meant for a quick look, not for resolution assessment — and if raw data is no longer on disk, the preview may be all that's left.

For a proper look at diffraction images, use one of the dedicated viewers on the beamline workstations: exact invocation to be confirmed for the LS-CAT environment

Viewer	Good for
DIALS image viewer	`dials.image_viewer *master.h5`
ADXV	`adxv *.h5`
ALBULA (DECTRIS)	PILATUS and EIGER detector data

With today's fast, fine-sliced detectors, a single image often shows very few spots — viewing several images together as a slab usually gives a much better sense of the diffraction.

Crystal snapshots (optical camera images) are viewable the same way, showing the centered crosshair and expected beam profile. Sample actions (washing, annealing) and robot loads each get their own set of documentation images too.

Per-image analysis plot

This plot tracks three things across a dataset, image by image: total spots found (yellow), spots identified as Bragg diffraction (blue), and an estimated resolution (red). Spot-finding uses DIALS; a resolution reading of −1 usually means too few spots to make an estimate, or a real data quality problem. A dip-and-recovery pattern often indicates sample rotation; a steady decline in spot count across the full rotation is a sign of radiation damage — cross-check against the radiation damage plot.

$A data collection's detail view in SynchWeb, showing the beamline parameters panel, diffraction image, crystal snapshot, and per-image analysis plot$

A data collection's detail view: collection parameters (left), the diffraction image and crystal snapshot (center), and the per-image spot/resolution plot (right).

Permalinks

Click the chain icon next to a dataset to generate a permanent link (it appears in your browser's address bar). Unlike most links inside a visit, a permalink won't change over time, so it's the right one to share with a collaborator on the same proposal or with LS-CAT staff.