Slide Scanner · Zeiss
A fully automated high-throughput slide scanning system. With a 100-slide capacity, 7-LED illumination, and 10×/20×/40× objectives, it is ideal for large cohort tissue section studies in both brightfield and fluorescence.
Instrument Features
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100-Slide Automated Magazine
Motorized slide loader holds up to 100 standard slides. Fully automated loading, scanning, and unloading allows unattended overnight batch runs — ideal for large cohort studies, clinical samples, or high-throughput screening.
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7-LED Illumination
7 independently controlled LED channels cover UV through far-red wavelengths. LED illumination provides instant on/off switching, consistent intensity, and long operational lifetime. Supports DAPI, GFP/FITC, TRITC/Cy3, Cy5, and transmitted light channels.
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10× / 20× / 40× Objectives
Three objective magnifications for flexible resolution and throughput trade-offs. 10× for overview tissue architecture and large-area mapping, 20× for cellular resolution across whole sections, 40× for subcellular detail in targeted regions.
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Brightfield & Fluorescence
Supports H&E, IHC (brightfield), and multi-channel fluorescence scanning in a single run. Transmitted light mode for standard histological stains; reflected light for fluorescent tissue sections, IF-stained slides, and FISH.
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Automated Focus & Tissue Detection
Hardware autofocus and automated tissue detection algorithms locate and scan only the tissue area on each slide, reducing scan time and file sizes. Z-stack scanning available for thick sections or 3D tissue analysis.
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ZEN Slidescan Software
Centralized batch management, scan profile creation, and image stitching. Outputs standard CZI or OME-TIFF files compatible with ImageJ, QuPath, HALO, and other image analysis platforms for downstream quantification.
Startup Guide
Power On System & LEDs
Turn on the Axioscan main power and the LED controller. Power on the PC. Launch ZEN Slidescan software. Allow 10–15 min warm-up for LED stabilization.
Prepare & Load Slides
Ensure all slides are clean, dry, and free of debris. Slides must be standard 75×25 mm. Label each slide position in the magazine log. Load slides into the magazine slots in order, coverslip side up. Slide the magazine into the instrument.
Create a Scan Profile
In ZEN Slidescan, create a new experiment. Select your objective (10×, 20×, or 40×). Configure fluorescence channels (LED line, filter cube, exposure time) or brightfield settings. Set Z-stack parameters if needed.
Set Focus Strategy
Select your focus strategy: hardware autofocus (fast, recommended for most slides) or contrast-based software autofocus. Set focus map density based on section flatness — increase density for wrinkled or thick sections.
Run Tissue Detection Pre-Scan
Run a rapid overview pre-scan (10× or lower) to detect tissue areas on each slide. Review detected regions in the ZEN tile editor and manually adjust any missed areas before starting the full scan.
Set Output & Storage
Confirm output file format (CZI recommended) and destination folder. Ensure sufficient disk space — multi-channel 40× scans of whole slides can reach 2–10 GB per slide. Set file naming convention for easy batch identification.
Start Batch Scan
Assign your scan profile to all slides in the batch. Start the automated run. The system will load, scan, and unload each slide sequentially. Monitor the first 2–3 slides to confirm focus and exposure are correct before leaving for unattended scanning.
Review & Export
After scanning, review images in ZEN Slidescan viewer. Export to TIFF, OME-TIFF, or BigTIFF for use in QuPath, HALO, or ImageJ. Archive raw CZI files to your lab storage before clearing the instrument data drive.
Shut Down
Remove slide magazine and retrieve your slides. Close ZEN Slidescan. Turn off the system per the posted shutdown checklist. Log your session in the instrument usage log.
💡 For large batches (50–100 slides), schedule an overnight run. Contact Adeela to coordinate — unattended overnight scans must be pre-approved and the output drive must be cleared beforehand.