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Nanolive 3D Cell Explorer User Manual (Analysis & Translation)

Product: Nanolive 3D Cell Explorer (incl. 3D Cell Explorer-fluo)
Original manufacturer: Nanolive SA (Lausanne, Switzerland) β€” www.nanolive.ch
Structure: 9 chapters / 60 pages / 16 selected figures

1. What is it? πŸ”¬

The 3D Cell Explorer is Nanolive's label-free live-cell 3D tomographic microscope based on Holographic Tomography. A Class I laser (Ξ»=520 nm, 0.2 mW/mmΒ² sample exposure, non-phototoxic) passes through live cells, and the refractive index (RI) distribution is recorded to reconstruct the cell's 3D internal structure.

1.1 Three major differences from conventional microscopes

Dimension Conventional microscope 3D Cell Explorer
Labeling Requires fluorescence/staining Fully label-free (RI-based)
Dimensionality 2D or confocal 3D (sectioning required) Single-shot 3D reconstruction (0.5 fps)
Phototoxicity Laser/mercury/LED damages cells Class I laser, 0.2 mW/mmΒ², no phototoxicity for long-term live-cell imaging
Data Grayscale + fluorescence channels 3D RI volume + digital staining (physical-parameter-based, quantifiable)

1.2 Two versions

1.3 Package contents (16 items)

# Item Qty
1 3D Cell Explorer main unit 1
2-5 USB 2.0 + USB 3.0 + power + IEC cables 1 each
6 Cleaning kit 1
7 Reusable dust cover 1
8 WEEE certificate 1
9 Microscope objective (MO) protective cap 1
10 BNC cable (fluo only) 1
11-16 CoolLED illumination system (fluo only): LED source + DC power + IEC cable + USB 2.0 + Liquid Light Guide (LLG) + 3 excitation filter holders 1 each

2. Instrument overview πŸ“·

2.1 Three views

Fig 1 β€” Front, side, and rear views of 3D Cell Explorer

Fig 1 β€” Three external views showing rotating arm, XY stage, scanning head, camera, and bottom interface layout.

2.2 Key components terminology

Fig 2 β€” Key components with labels

Fig 2 β€” 7 core components: Scanning head / Rotating arm / XY stage / Z knob (focus) / Microscope objective (60X NA 0.8) / Camera (CMOS 1024Γ—1024 @ 165 fps) / Peripheral mirror (for 3D tomography)

2.3 Fluo version and CoolLED

3D Cell Explorer-fluo overview

Fluo version: same external shape as base, with additional LLG liquid light guide port and BNC trigger on the back.

CoolLED illumination system

CoolLED pE-800 series: supports 3-4 excitation filters simultaneously (DAPI/FitC/TritC/Cy5), switch time <100 ΞΌs, lifetime >20,000 h per channel.

3. Technical specifications πŸ“‹

3.1 Base version

Spec Value Note
Dimensions (WΓ—DΓ—H) 380Γ—170Γ—445 mm Desktop
Weight 8 kg Single-person portable
Operating temp 20-30Β°C / 100-240 VAC / 50-60 Hz / 1.0-0.5 A Temperature control critical
Camera CMOS 165 fps, 1024Γ—1024 px, USB 3.0 Native sampling
Objective 60X, dry (non-oil) Maintenance-free
Laser Class I (Ξ»=520 nm, 0.2 mW/mmΒ²) No goggles needed
FoV 85Γ—85Γ—30 Β΅m Per 3D reconstruction
Lateral resolution 200 nm Sub-cellular
Axial resolution 400 nm
Tomography frame rate 0.5 fps (one full 3D every 2 s)
Self-adjustment time <90 s Depends on optical thickness

3.2 Fluo version + CoolLED

Spec Holographic tomography Fluorescence
Dimensions 380Γ—170Γ—445 mm 77Γ—186Γ—162 mm (CoolLED controller)
Weight 8 kg 4 kg
Operating temp 20-30Β°C 5-35Β°C
Camera USB3.0 CMOS Sony IMX174 (QE 70% @545 nm, dark noise 6.6 e⁻, DR 73.7 dB) β€”
FoV 90Γ—90Γ—30 Β΅m 90Γ—90 Β΅m
Lateral res 200 nm 400 nm
Channels up to 7 simultaneous (RI digital stains) 3 fluorescence (3 std / 4 max)
Frame rate 0.5 fps 3 fps/channel
Filters β€” Std: FitC+TritC+DAPI or FitC+TritC+Cy5; Full 4: TritC and Cy5 interchangeable on channel 3

3.3 Computer requirements (mandatory)

⚠️ GPU is the hard threshold β€” without NVIDIA discrete 8 GB, STEVE cannot run full version.

Item Minimum
CPU 2.0 GHz quad-core or faster
RAM 16 GB DDR3
Storage 2 GB system for STEVE + separate 1 TB data drive (continuous @0.5 fps = 1-2 GB/h)
GPU NVIDIA discrete 8 GB VRAM (4 GB insufficient)
USB At least 1 USB 3.0 port (for camera)
OS Windows 10 64-bit + latest NVIDIA drivers + USB 3.0 drivers
Network Internet for installation

πŸ’‘ Supplier can provide a tested/validated PC/laptop list (manual P15) β€” request before purchasing.

4. First start-up β€” 9 physical installation steps πŸ”Œ

4.1 Unboxing and positioning

Fig 3 β€” Package contents

Fig 3 β€” 16 package items. Fluo adds BNC cable and CoolLED system.

Step 1: Place on stable, flat, level, sturdy bench. Hold by base or sides β€” never lift by camera (P19 warning). Misuse damage not covered by warranty.

Step 2: Remove disposable plastic wrap and red vinyl MO cap.

4.2 CoolLED wiring (fluo only)

⚠️ Safety first β€” do not connect main power before LLG is installed.

Step 3: Place CoolLED near microscope, 200 mm clearance on each side for cooling (P22 Fig d).

Step 4: Insert 3 excitation filter holders (DAPI/FitC/TritC or Cy5) into CoolLED top slots, note orientation (P21).

Steps 5-6: Install LLG at CoolLED end.

Fig a β€” LLG end cap removal

Fig a β€” Remove red vinyl cap from LLG end.

Fig b/c/d β€” LLG into CoolLED + CoolLED placement

Fig b β€” Insert LLG fully into CoolLED top port, secure with 1.5 mm hex key (don't over-torque β€” damages LLG head, reduces coupling).
Fig c/d β€” CoolLED with LLG installed, placed vertically with 200 mm clearance.

Step 7: Install LLG at microscope end.

Fig g β€” LLG into 3D Cell Explorer-fluo microscope

Fig g β€” LLG other end into microscope side port, 3 set screws tightened in sequence. Any physical damage to LLG head causes irreversible loss of coupling efficiency.

πŸ’‘ LLG bend radius rule (P24 Fig i/j):

  • Short-term bend R >40 mm
  • Long-term bend R >75 mm
  • 90 mm verified stable
  • Never stretch, kink, or contact sharp objects β€” internal glass fibers break β†’ reduced light output

Steps 8-9: Connect CoolLED power (DC PSU β†’ CoolLED, plug flat side inward P25 Fig m) + USB 2.0 (CoolLED β†’ PC) + BNC (CoolLED β†’ microscope trigger).

4.3 Main unit power + USB

Step Action Notes
1 USB 3.0: microscope side β†’ PC Tighten screws, must use PC's USB 3.0 port (not 2.0)
2 USB 2.0: microscope back β†’ PC Any USB port
3 Power β†’ PSU β†’ outlet Confirm power switch off before plugging
4 Fluo: CoolLED power β†’ IEC β†’ outlet CoolLED has no power switch β€” plugging in powers it

4.4 Install STEVE software

Go to www.nanolive.ch/register (serial number on unit bottom / delivery note / quick start guide), download STEVE. Important: right-click STEVE.exe β†’ "Run with graphics processor" β†’ select "Nvidia high-performance" (integrated GPU = very slow).

5. Correct moving/transport ⚠️

P30-P37 β€” transport protection; customers often damage units by ignoring these.

5.1 Before moving

  1. Unplug all cables: power + USB 2.0 + USB 3.0 (fluo: add BNC + LLG)
  2. Use Z knob to raise stage to top position (otherwise hits MO during move)
  3. Lock stage with red set screw
  4. Fluo: cap LLG ends with red vinyl caps + cap MO with black vinyl cap

5.2 Stage locking

Stage locking diagram

Left = high-damage transport position (stage not raised). Right = correct (Z knob up + red set screw locked).

Red set screw position

Red set screw location. Must remove together when disassembling stage.

5.3 Carrying position

P37: hold bottom or sides β€” never lift by stage, rotating arm, or camera.

5.4 LLG end protection

6. Sample preparation 🧫

P38 summary; detailed SOP in supplier's Nanolive Sample Preparation Protocol and Nanolive's Best Staining Practices (English).

6.1 Compatible containers

Container Use case
Glass coverslip Fixed cells (after attachment)
FluoroDishβ„’ Live-cell long-term imaging (preferred)

Not suitable: non-glass-bottom plastic plates, suspension cells in droplets (optical path through liquid column attenuates).

6.2 Key rules

7. Optical cleaning procedure 🧹

P39-P40: cleaning is the only user-serviceable maintenance; other disassembly voids warranty.

General rules:

7.1 Microscope objective (most frequent)

Fig 7 β€” MO cleaning

Fig 7 β€” MO is most contamination-prone (sample sits on it); needs regular cleaning.

7.2 Rotating arm scanning mirror (occasional)

Fig 8 β€” Scanning mirror cleaning

Fig 8 β€” Scanning mirror on rotating arm: less exposed, infrequent cleaning.

7.3 Rotating arm center mirror (least frequent)

Fig 9 β€” Center mirror cleaning

Fig 9 β€” Center mirror not exposed, occasional cleaning only.

πŸ’‘ When not in use, strongly recommend red vinyl cap on MO (P33) β€” prevention is easier than cleaning.

8. STEVE software β€” acquisition and digital staining 🎨

P41-P55. STEVE = Software for Tomographic Explorer for Visualization and Evaluation.

8.1 Core features

Module Function
Microscope control Single 3D, time-lapse 3D, bright-field assistant, fully auto self-adjust
2D view X-Y slice + user-defined staining overlay
3D view 3D volume rendering (voxel/surface) + screenshot + AVI recording
Digital staining RI-based (not color) physical staining β€” quantifiable
Data export raw/tiff/obj/png/jpeg + proprietary .vol/.vo1x
Annotation Custom properties per measurement
Semi-auto update New version auto-prompts; close β†’ maintenance tool β†’ update component

8.2 Software UI (Fig 10)

Fig 10 β€” STEVE main interface

Fig 10 β€” STEVE UI: β‘  2D view (left) β‘‘ 3D view (top right) β‘’ Panel viewer (bottom center, RI Γ— RI-gradient 2D space) β‘£ Stain picker (bottom right) β‘€ Button area + sliders + timeline + stain properties.

8.3 Complete acquisition workflow

  1. Open STEVE β†’ power on 3D Cell Explorer β†’ wait for auto-detection (USB 3.0 must be correctly connected, otherwise Connection failure err.3.3)
  2. Bright-field selection β†’ use microscope XY+Z knobs to find cell (bright-field is for search only, not for data acquisition)
  3. Select immersion medium β†’ STEVE prompts for RI (water / DMEM / custom) β€” wrong = blurry reconstruction
  4. Single acquisition β†’ click "3D" button or Microscope β†’ Single Shot β†’ select RI β†’ auto-starts (0.5 fps = 2 s result)
  5. Digital staining β†’ draw ROI in 2D view β†’ pick color β†’ stain appears in panel viewer
  6. Save β†’ Save button β†’ default .vol format (only STEVE can read)

8.4 Time-lapse

Click "4D" button or Microscope β†’ Time Lapse β†’ 2 dialogs:

Can set auto-stop or manual-stop.

8.5 Digital staining β€” STEVE's soul

Why important: raw data is a 3D RI volume (looks grayscale); digital staining lets you "color-code different RI values" = label-free multiplexed immunofluorescence.

10 steps (P51-P52):

  1. Select meaningful slice (drag in 2D view / slider)
  2. "+" new stain
  3. Name (optional)
  4. Pick color
  5. Draw ROI in 2D view (pixels light up; release mouse β†’ stain range calculated)
  6. Stain shows in panel viewer (RI Γ— RI-gradient space)
  7. Adjust opacity / edge softness / shape
  8. Add more stains β†’ repeat
  9. One acquisition = up to 7 RI digital stains + 3 fluorescence = 10 simultaneous markers
  10. Stain can be hidden / deleted / recolored

πŸ’‘ Digital staining precision depends on sample preparation RI uniformity β€” see Best Staining Practices (P56 download link).

8.6 Save and export

Fig 16 β€” Save dialog

Fig 16 β€” Save button β†’ default .vol.

Fig 17 β€” Export settings

Fig 17 β€” File β†’ Export β†’ range (single/all/every N frames), data type (RI/fluorescence), format (raw/tiff/obj/png-jpeg).

Notes:

9. Troubleshooting πŸ”§

P57-P58 error code list:

Code Module Cause + Fix
err.1.1 Calibration failed Too much liquid above sample / rotating arm path blocked / dish wall blocks beam β†’ move to dish center
err.1.4 Calibration failed Sample absorbs too much (dense dye/thick tissue) β†’ move or contact supplier
err.2.1 Acquisition failed Position bad β†’ move region / clean MO / check sample prep
err.3.1 Connection failed USB 2.0 loose / scope not powered β†’ restart PC + replug
err.3.2 Connection failed USB 3.0 not tightened / not in PC USB 3.0 port
err.3.3 Connection failed USB 3.0 line detected as USB 2.0 (driver issue) β†’ try other port / install USB 3.0 driver
err.3.4 Connection failed Scope init failed (rotating arm blocked) β†’ power off β†’ check arm free rotation
err.3.6 Connection failed Scope needs service β†’ contact supplier
err.3.7 Connection failed (fluo) Fluorescence module connection failed β†’ check CoolLED power + USB
err.3.8 Connection failed Firmware update error β†’ contact support
err.5.1 Processing failed GPU doesn't meet requirement (at least NVIDIA 2 GB discrete VRAM) β†’ update NVIDIA driver

10. Safety/regulatory essentials ⚠️

P1-P5 β€” must read, customers often ignore.

  1. Class I laser (Ξ»=520 nm): harmless to eyes, but no unauthorized opening of cover to access laser path
  2. CoolLED source (fluo only): may emit UV (depends on wavelength config) β†’ don't look directly + don't cover light guide (fire risk)
  3. EN/IEC 61010-1:2010 + EN62471:2008 dual certification (light source risk group 3)
  4. No flammable/toxic solvents for cleaning; ethanol/isopropanol OK (away from ignition, ventilated)
  5. Not for humid environments
  6. User responsible for bio-contamination prevention (clean after each use)
  7. Disconnect power before any maintenance

11. Key resources πŸ”—

πŸ“₯ Original PDF

πŸ“„ 3D Cell Explorer User Manual PDF (Chinese version, 60 pages, 2.2 MB)

Contact｜Li Dongwei (李东伟)
πŸ“ž 18045130660
🌐 Website: https://www.biokingdom.top