What are the microscope requirements for the SeekSpace workflow?
2026-06-23
Answer:
SeekSpace workflows require a fluorescence-capable microscope for imaging both H&E-stained and ssDNA-stained tissue sections.
High-quality tissue imaging is important because downstream spatial reconstruction and visualization rely on accurate alignment between:
- Tissue morphology
- Nuclear distribution patterns
- Spatial barcode coordinates
- Gene expression data
H&E images are primarily used for tissue integrity assessment and nuclei evaluation, while ssDNA fluorescence images are used for tissue boundary definition and spatial registration.
Required imaging channels
Imaging Type | Recommended Mode |
H&E imaging | Brightfield / transmitted light imaging |
ssDNA imaging | FITC/GFP fluorescence channel |
For ssDNA imaging, the recommended fluorescence configuration is:
- Excitation: 480/40 nm
- Emission: 535/50 nm
Recommended microscope configuration
Parameter | Recommended Requirement |
Slide scanning range | At least 76 × 26 mm |
Objective lens | 10× objective, NA > 0.3 recommended |
Focus mode | Manual focus and/or real-time autofocus |
Motorized Z-axis | Recommended for multi-point focus adjustment |
Camera bit depth | Monochrome ≥8-bit or color camera with monochrome mode ≥3×8-bit |
Image stitching | Adjustable stitching supported |
Overlap ratio | Adjustable; ~10% recommended |
Shade correction | Adjustable |
Export format | TIFF export supported |
Minimum stitched image size | ≥12000 px (length) × ≥4340 px (width) |
The camera resolution should appropriately match the theoretical optical resolution of the objective lens. Consultation with the microscope manufacturer is recommended for detailed hardware matching.
Recommended microscope models
SeekSpace has validated compatibility with several commonly used imaging systems, including:
- Leica DMi8
- Keyence BZX800
- Thermo Fisher EVOS M7000
- Olympus BX53
Equivalent systems with comparable imaging performance may also be suitable.
Imaging quality recommendations
To ensure stable downstream spatial analysis:
- Tissue sections should remain flat and parallel to the stage during imaging.
- Exposure settings should avoid both underexposure and overexposure.
- Focus points should be selected within tissue-covered regions, ideally spanning all four corners of the slide.
- Tissue edges and boundary regions should remain clearly visible in fluorescence images.
- Slides should not be exposed to excitation light for prolonged periods to minimize photobleaching.
- Images should be reviewed immediately after acquisition and retaken if image quality is insufficient.
Computational recommendations
Because stitched fluorescence images may contain thousands of image tiles, the microscope workstation should have sufficient computational resources for image processing.
Recommended minimum workstation specification:
- ≥16 GB RAM
- Adequate CPU performance for large-image stitching and TIFF export
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