Microscope Selection Guide

OBC Microscope Selector
๐Ÿ”ฌ UCI Optical Biology Core

Microscope Selection Guide

Answer a few quick questions and we’ll recommend the best instrument for your research needs.

Step 1 of 5
Question 1 of 5
What type of sample are you imaging?
This helps us determine which systems are compatible with your specimen.
Question 2 of 5
What level of resolution do you need?
Standard confocal resolution is ~250nm. Super-resolution goes much further.
Question 3 of 5
How many fluorescent markers are you using?
Multiplexing โ€” imaging multiple markers simultaneously โ€” requires specialized detection capabilities.
Question 4 of 5
Do you need time-lapse or live imaging?
Some experiments require imaging the same sample over hours, days, or weeks.
Question 5 of 5
What is your microscopy experience level?
This helps us recommend the right level of support alongside your instrument recommendation.
Not sure? Contact Adeela Syed (adeelas@uci.edu) for a personal consultation.
All instruments available 24/7 โ€” book through iLab Solutions.
const answers = {}; const totalSteps = 5; function select(btn, step, value) { const group = btn.closest(‘.options’); group.querySelectorAll(‘.opt-btn’).forEach(b => b.classList.remove(‘selected’)); btn.classList.add(‘selected’); answers[step] = value; const nextBtn = document.getElementById(‘next’ + step.replace(‘s’,”)); if (nextBtn) { nextBtn.classList.add(‘enabled’); } } function nextStep(current) { if (!answers[‘s’+current]) return; document.getElementById(‘step’+current).classList.remove(‘active’); document.getElementById(‘step’+(current+1)).classList.add(‘active’); updateProgress(current+1); } function prevStep(current) { document.getElementById(‘step’+current).classList.remove(‘active’); document.getElementById(‘step’+(current-1)).classList.add(‘active’); updateProgress(current-1); } function updateProgress(step) { const pct = ((step-1) / totalSteps) * 100; document.getElementById(‘progressFill’).style.width = pct + ‘%’; document.getElementById(‘progressLabel’).textContent = ‘Step ‘ + step + ‘ of ‘ + totalSteps; } function showResult() { document.getElementById(‘step5’).classList.remove(‘active’); document.getElementById(‘resultPanel’).classList.add(‘active’); updateProgress(5); document.getElementById(‘progressFill’).style.width = ‘100%’; document.getElementById(‘progressLabel’).textContent = ‘Complete โœ“’; const s1 = answers[‘s1’]; const s2 = answers[‘s2’]; const s3 = answers[‘s3’]; const s4 = answers[‘s4’]; const s5 = answers[‘s5’]; let rec = ”, why = ”, also = [], support = ”; // Slide scanner if (s1 === ‘slides’) { rec = ‘Zeiss Axioscan’; why = ‘With up to 100 slides per automated run, the Axioscan is purpose-built for your needs. It images tissue sections unattended overnight or over weekends, freeing you to focus on analysis rather than sitting at a microscope.’; also = [‘Zeiss LSM 900 (spot checking)’, ‘Leica SP8′]; } // Large cleared tissue else if (s1 === ’tissue’) { rec = ‘Zeiss Lightsheet Z.1’; why = ‘The Lightsheet Z.1 is specifically designed for mesoscale imaging of large cleared tissue specimens and whole organs. Its light sheet illumination minimizes photobleaching and phototoxicity across the entire volume, and on-campus users benefit from a daily billing cap of $125.’; also = [‘Zeiss LSM 980 (smaller regions)’, ‘Zeiss Axioscan (2D sections)’]; } // Expansion microscopy else if (s1 === ‘expanded’) { if (s3 === ‘many’) { rec = ‘Zeiss LSM 980 + Leica Stellaris’; why = ‘For expansion microscopy with complex multi-marker panels, the LSM 980\’s 32-channel spectral detector enables linear unmixing of multiple fluorophores with minimal crosstalk. For markers with overlapping emission spectra, the Leica Stellaris at UCI adds FLIM-based separation โ€” distinguishing fluorophores by their unique excited-state lifetime rather than emission wavelength alone.’; also = [‘Zeiss LSM 780’, ‘Zeiss LSM 900’]; } else { rec = ‘Zeiss LSM 980’; why = ‘For expansion microscopy, the LSM 980 with its 32-channel spectral detector is the ideal choice. The physical expansion of the sample provides enhanced resolution, and the spectral detector ensures accurate co-detection of your developmental markers within the expanded specimen.’; also = [‘Zeiss LSM 780’, ‘Leica SP8’]; } } // Super-resolution else if (s2 === ‘superres’) { rec = ‘Zeiss Elyra 7 Lattice SIMยฒ’; why = ‘The Elyra 7 is our dedicated super-resolution system. With Lattice SIMยฒ processing it achieves 60nm resolution, and with Single Molecule Localization Microscopy (SMLM) it resolves molecular details down to approximately 20nm โ€” ideal for visualizing nanoscale cellular structures that are invisible to standard confocal systems.’; also = [‘Zeiss LSM 980 with Airyscan 2 (120nm)’, ‘Zeiss LSM 900 with Airyscan 2’]; } // Live + long timelapse else if ((s1 === ‘live’) && s4 === ‘long’) { rec = ‘Zeiss LSM 980’; why = ‘The LSM 980 is equipped with a CO2 incubator and environmental control system, making it the top choice for overnight and weekend time-lapse experiments. Its overnight billing cap and weekend rate structure (billed at only 5 hours per 24-hour period) make extended live imaging experiments highly cost-effective.’; also = [‘Zeiss LSM 780 (live incubation)’, ‘Leica SP8’]; } // Highly multiplexed else if (s3 === ‘many’) { rec = ‘Zeiss LSM 980’; why = ‘For highly multiplexed experiments with 5 or more fluorophores or spectrally overlapping dyes, the LSM 980\’s 32-channel spectral detector enables linear unmixing across all channels simultaneously, minimizing crosstalk and ensuring accurate signal separation. As a complementary option, the Leica Stellaris adds FLIM-based fluorophore separation for experiments where spectral overlap cannot be resolved by unmixing alone.’; also = [‘Leica Stellaris (FLIM)’, ‘Zeiss LSM 780’]; } // Enhanced resolution else if (s2 === ‘enhanced’) { rec = ‘Zeiss LSM 980 with Airyscan 2’; why = ‘The LSM 980\’s Airyscan 2 detector delivers super-resolution imaging up to 120nm โ€” approximately twice the resolution of standard confocal โ€” without sacrificing speed or signal-to-noise ratio. It is the ideal balance between resolution, sensitivity, and throughput for most demanding cell biology applications.’; also = [‘Zeiss LSM 900 with Airyscan 2’, ‘Zeiss Elyra 7 (if 60nm needed)’]; } // Standard fixed, few markers else if (s1 === ‘fixed’ && s3 === ‘one’) { rec = ‘Leica SP8 or Zeiss LSM 900’; why = ‘For straightforward fixed sample imaging with 1โ€“2 markers at standard confocal resolution, the Leica SP8 and LSM 900 are both excellent, cost-effective options. The SP8 offers 6 laser lines and 4 detectors for maximum flexibility, while the LSM 900 provides Airyscan capability if you later need enhanced resolution.’; also = [‘Zeiss LSM 780’, ‘Zeiss LSM 980’]; } // Default else { rec = ‘Zeiss LSM 980’; why = ‘Based on your requirements, the LSM 980 is our most versatile and capable confocal system. It combines a 32-channel spectral detector for multiplexed imaging, Airyscan 2 super-resolution up to 120nm, 2-photon capability, live-cell incubation, and 2 Non-Descanned Detectors for thicker specimens โ€” making it the best all-around choice for a wide range of experiments.’; also = [‘Zeiss LSM 780’, ‘Zeiss LSM 900’, ‘Leica SP8’]; } // Support message if (s5 === ‘new’) { support = ‘๐ŸŒฑ As a new user, we recommend scheduling a training session with OBC staff before your first booking. Contact Adeela Syed at adeelas@uci.edu to arrange hands-on training.’; } else if (s5 === ‘intermediate’) { support = ‘๐Ÿ”ฌ We recommend a brief instrument-specific orientation session. OBC staff can walk you through the specific features of this system relevant to your experiment.’; } else { support = ‘๐ŸŽ“ As an experienced user, you can book directly through iLab and work independently. OBC staff are available if you have specific technical questions.’; } document.getElementById(‘resultContent’).innerHTML = `
Your Recommendation
๐Ÿ”ฌ
Best Match for Your Needs

${rec}

Based on your answers about sample type, resolution, multiplexing, time-lapse needs, and experience level

Why this instrument

${why}

${also.length ? `

Also worth considering

${also.map(a => `${a}`).join(”)}
` : ”}
Next Steps: ${support}
`; } function restart() { Object.keys(answers).forEach(k => delete answers[k]); document.getElementById(‘resultPanel’).classList.remove(‘active’); document.querySelectorAll(‘.step’).forEach(s => s.classList.remove(‘active’)); document.querySelectorAll(‘.opt-btn’).forEach(b => b.classList.remove(‘selected’)); document.querySelectorAll(‘.next-btn’).forEach(b => { b.classList.remove(‘enabled’); }); document.getElementById(‘next5’).classList.add(‘enabled’); document.getElementById(‘step1’).classList.add(‘active’); document.getElementById(‘progressFill’).style.width = ‘0%’; document.getElementById(‘progressLabel’).textContent = ‘Step 1 of 5’; }
Scroll to Top