Across-scales imaging is easy to promise and hard to deliver. Core Imaging Labs are being asked for three things at once; native-state preservation, context-rich views of real biology, and increased throughput. Add the need to correlate with EM (cryo-FIB/cryo-ET), FM and sometimes chemistry-aware tools (SIMS, Raman), and the result is too often contaminated samples, long queues, and costly “null” tomograms.

The SiriusXT thesis: insert a context layer between fluorescence and EM. Use it to scout in native state, decide where high-resolution hours should be spent, and route regions of interest to the right downstream processes. The context layer is soft X-ray tomography (SXT) generated—whole-cell volumes imaged at ~50 nm isotropic resolution through ~10 µm thickness, with native contrast and no stains or sectioning.

The ideal workflow

Start with vitrified samples on standard EM carriers. Capture functional markers in FM. Move to SXT to scout in 3D—see organelles, membranes, and overall architecture in the cell’s native state. Decide on regions of interest (ROIs) with FM–SXT alignment and precisely capture these ROIs in cryo-FIB generated lamellae for high-resolution analysis by cryo-ET. When chemistry matters, branch to SIMS/Raman on the same carriers, guided by the same ROI map. Quantify, correlate, and report with a metadata trail that survives every hand-off.

What changes when you scout first (with SXT):

• Fewer dead-end lamellae. Targeted prep replaces hope.
• Shorter, more predictable queues. EM hours are spent only where they count.
• Better stories from your data. Structure, function, and chemistry line up in space.
• Happier PIs. Native-state evidence plus turnaround times they can plan around.

Four concrete workflows that show the breadth!

1. Antiviral efficacy in hepatitis-C.

To test whether a therapy truly reverses disease phenotypes, infected hepatocytes are vitrified and tagged in FM for viral proteins. SXT volumes reveal ultrastructural morphology—ER rearrangements, replication organelles, mitochondria and lipid droplet remodelling—and highlight cells trending back toward healthy morphologies. Targeted cell regions are captured in a cryo-FIB produced in-situ lamella for subsequent cryo-ET, where restored organelle architecture becomes the proof-point for therapeutic effectiveness.

2. Thyroid organoids with ciliogenesis defects.

High-pressure frozen organoids are sliced by cryo-FIB into 5–8 µm thick slabs using a cryo—lift-out technique. SXT scouts the slabs to flag follicles lacking apical cilia. Only those are thinned further into 150 nm lamellae, then imaged by cryo-ET to resolve transition-zone architecture. The pipeline turns a low-frequency phenotype into a tractable, high-yield workflow.

3. Viral assembly intermediates in infected cells.

Cells are high-pressure frozen on TEM grids using the waffle method. Cryo-FM offers clues, but rapid SXT mosaics across the grid pinpoint rare patches where capsid assembly is underway. A cryo-FIB lamella is cut through one of these budding sites and cryo-ET resolves the capsid lattice and membrane remodeling in situ. The SXT scouting step makes rare-event capture reproducible.

4. Nanomedicine delivery and endosomal escape.

FM-SXT reveals where nanoparticles go; SXT shows the ultrastructural context—endosomal crowding, membrane disruptions, organelle responses. Escape-positive regions are prioritised for cryo-FIB and cryo-ET to visualise vesicle rupture or pore formation. The same ROI can be branched to SIMS/OrbiSIMS for molecular maps, creating a complete structure–function–chemistry story.

Interoperability is non-negotiable!

The SXT-100 was built as a platform layer: same cryo carriers you already use; integrated multi-colour fluorescence for quick screening and co-registration; clean coordinate hand-offs to FIB-SEM, cryo-TEM, and chemistry modalities. Think of it as your planning microscope: the place where context becomes a decision.

If you manage a Core Imaging Lab, a few KPIs worth tracking

• EM hit-rate after SXT triage (% of lamellae yielding informative tomograms)
• Queue time from intake to EM acquisition
• Null-tomogram rate
• Sample loss/contamination events per 100 transfers
• Structure–function–chemistry co-registration success (%)

When these trend in the right direction, research publications increase—and people notice.

The X-factor!

Across-scales shouldn’t require heroics. With a context layer in the middle, it becomes a repeatable workflow rather than a one-off achievement. If you’re building or upgrading a cryo-correlative imaging pipeline, we’ve got some great tips and images to demonstrate the benefits of CLE’X’M—happy to share these and to provide more information on the above-mentioned workflows with you in a Zoom call. Get in touch – Book a Demo!

Check out our images gallery to learn more about the power of Soft X-ray Tomography!