# Nikon Eclipse Ti2-E with AX R MP Confocal/Multiphoton System

## System Reference for Imaging & Microscopy Workflows

This document describes a fully motorised inverted microscope platform (Nikon Eclipse Ti2-E) coupled with an AX R multiphoton/confocal scan head, a dual-output tuneable IR laser, six-line visible laser unit, NSPARC super-resolution detector, FLIM capability, and environmental control. It is intended as a machine-readable reference for designing acquisition workflows, analysis pipelines, and experiment planning with LLM-based tools.

---

## 1. Microscope Stand

### 1.1 Main Body — Eclipse Ti2-E (MEA54000)

- Inverted configuration.
- Motorised built-in encoded Z-drive: 10 nm step (open loop), 20 nm step (closed loop).
- Motorised light-path change with positions: Left 100 %, Eyepiece 100 %, Right 100 %, Left/Eye 80/20 %.
- Built-in Bertrand lens (encoded).
- Encoded 1×/1.5× tube lens.
- Field Number 25 at left/right ports.

### 1.2 Eyepiece Assembly

| Component | Code | Description |
|---|---|---|
| S Tube | MEB52340 | Inclination 35°, interpupillary distance 50–75 mm |
| BC Port Eyepiece Tube Base | MEB55855 | 16 mm FOV camera port; accepts 0.55× C-mount directly or C-mount with LV-TV adapter; low-weight/small-footprint cameras |
| Eyepieces (×2) | MAK10110 | CFI 10×22 with dioptre adjustment |

### 1.3 Nosepiece — Perfect Focus System

| Component | Code | Description |
|---|---|---|
| PFS + Motorised Nosepiece for MP | MEP59395 | TI2-N-NDM-P Perfect Focus Unit v4 with altered notch filter for multiphoton use; two-part PFS4 for stability; integrated liquid-leak protection tray; overflow tube |

### 1.4 Stage & Accessories

| Component | Code | Description |
|---|---|---|
| Motorised Stage with Encoders | MEC56120 | XY travel: ±57 mm (X) × ±36.5 mm (Y) = 114 × 73 mm total; speed 25 mm/s; minimal step 100 nm; repeatability ±500 nm; connects directly to Ti2-E controller |
| Stage-Up Kit | MED53210 | Enables dual-layer configuration (Ti2-E only; not compatible with Ti2-A/Ti2-U) |
| Stage Joystick | MEF55706 | TI2-S-JS-SS |

### 1.5 Condenser

| Component | Code | Description |
|---|---|---|
| Motorised Condenser Turret | MEL51920 | TI2-C-TC-E |
| LWD Lens System | MEL56200 | NA 0.52, WD 30 mm, objectives 4–100× |

### 1.6 DIC Optics

| Component | Code | Description |
|---|---|---|
| DIC Slider 20×III | MBH76222 | Compatible with MRD77200 and MRD70270 |
| DIC Slider 40× I | MBH76240 | — |
| LWD Dry DIC Module | MEH51520 | TC-C-ML-N2D |
| DIC Slider 60× II | MBH76260 | — |
| Analyser Cube (Large FOV) | MEN51985 | Required for DIC with FOV > 18 mm |
| Intelligent Polariser | MEN51944 | Requires motorised or intelligent condenser |
| LWD DIC 4× Module | 1DM37150 | 1.5 mm aperture, 37 mm diameter; fits inside phase slots |
| LWD DIC 20× Aperture Module | 1DM37940 | 9.0 mm aperture, 37 mm diameter |

---

## 2. Widefield Fluorescence (Epi)

### 2.1 LED Illumination

| Component | Code | Description |
|---|---|---|
| D-LEDI System | MBF83000 | 4-channel LED: 385 nm, 475 nm, 550 nm, 621 nm; controllable via NIS-Elements or manual controller; brighter when attached directly (vs. fibre) |
| D-LEDI Ti2 Connection Cable | MXA22196 | Required for Ti2-E/A |
| AC Adapter (D-LEDI) | MQF52057 | Required power adapter |

### 2.2 Filter Turret & Filter Cube

| Component | Code | Description |
|---|---|---|
| Motorised Epi Filter Turret | MEV51030 | Holds six 32 mm or 25 mm filter cubes |
| Quad-band Filter Cube | MXR00252 | DAPI/FITC/TRITC/Cy5 BrightLine® "Full Multiband", ZERO™ Pixel Shift, LED-optimised; Exciter FF01-378/474/554/635-25; Emitter FF01-432/515/595/730-25-Z; Dichroic FF409/493/573/652-Di02-25×36-Z; 25 mm; mounted in TE2000 cube |

### 2.3 LAPP (Laser Application) Illumination Path

| Component | Code | Description |
|---|---|---|
| Fixed Main Branch | MEE54860 | For LAPP system; single module; no sub-branch; no field stop |
| Stage-Up Lens | MEV53004 | For use with LAPP + stage-up kit |
| EPI-FL Module | MEE54741 | TI2-LA-FL-3; NIR-compatible; 25 mm FOV; connects directly to D-LEDI; requires MXA22205 C-FIBA adapter for third-party fibre light sources |

### 2.4 Transmitted-Light Path

| Component | Code | Description |
|---|---|---|
| Pillar for Diascopic Illumination | MEE59925 | Holder for two fixed 45 mm filters; one position for PFS filter |
| AX LED Lamp House | MEE55855 | For use with DUT (MHE50350) |

---

## 3. Confocal / Multiphoton Scan Head

### 3.1 AX R MP Scan Head & Controller (MHA52300)

- Point-scanner with both confocal and multiphoton (MP) capability.
- 22 mm Field of View.
- **Galvano** mirror pair: high-resolution acquisitions up to **8192 × 8192**.
  - Max frame rate: 10 fps at 512 × 512 (bidirectional); 240 fps at 512 × 16 (band scan).
- **Resonant** mirror: high-throughput gentle imaging up to **2048 × 2048**.
  - Max frame rate (2K mode): 30 fps at 2048 × 512; 15 fps at 2048 × 1024; 7.5 fps at 2048 × 2048; 720 fps at 2048 × 16 (band scan).
  - Max frame rate (1K mode): 30 fps at 1024 × 512; 720 fps at 1024 × 16 (band scan).
- Scan modes: line scanning, bidirectional scanning, averaging.
- Simultaneous acquisition: max 5 channels (including diascopic detector channel).
- One VIS laser input, one IR laser input.
- First dichroic mirrors: 405/488/561/640 nm.
- Beam splitter: 20/80.
- IR composite dichroic mirror, gold mirror.
- Variable pinhole: 6–153 µm.
- Zoom: 1–1000× continuously variable.
- AI-powered acquisition parameter selection and visualisation.
- Upgradeable to: NSPARC super-resolution detector, confocal detection (with VIS laser + detectors), FLIM.

### 3.2 Scan-Head Accessories

| Component | Code | Description |
|---|---|---|
| Optional Output Laser Port | MHV56300 | 3rd outport AUX; required for third-party FLIM add-on |
| Resonant 2K Conversion Unit | MHE60310 | AD-R2K; connection board for resonant scanner up to 2048 × 2048 |
| Ti2 Adapter Set | MHV55710 | AX-TI2 |
| Ti2 Interlock Switch | MHV55730 | AX-TI2-ISW |

---

## 4. Detectors

### 4.1 Non-Descanned Detector (NDD) — Epi Direction (MHE60510)

- Collects emitted visible light in epi direction from IR-excited dyes (no confocal sectioning).
- Positioned directly after the objective for maximum light collection.
- Specific to inverted Ti2 + AXMP scan head.
- Detectable wavelength range: **400–750 nm** (1300 nm system configuration).
- Pre-equipped with **2 × GaAsP PMTs**; upgradeable to **4 channels** simultaneously (3 GaAsP + 1 multi-alkali also possible).

### 4.2 Additional NDD PMTs

| Component | Code | Qty | Description |
|---|---|---|---|
| GaAsP PMT (MP NDD) | MHE60530 | 2 | High-sensitivity, low-noise; green–orange wavelength range |

### 4.3 NDD Filter Cubes

| Filter Cube | Code | Bandpass |
|---|---|---|
| A1-F NDD 641/75 732/68 | MHE57821 | 641/75 + 732/68 |
| A1-F NDD 450/70 | MHE57801 | 450/70 |
| A1-F NDD 550/88 | MHE57811 | 550/88 |

### 4.4 Descanned Detector — DUX-VB4 4-Channel Unit (MHE60000)

- Tunable and high-sensitivity low-noise detectors.
- **4 detection paths**: 4 dyes simultaneously, up to 66 channels sequentially.
- 2 tunable detection paths + 2 filter-wheel detection paths.
- Detection range: **400–920 nm** (per-laser breakdown: 400–650 nm with IR laser, 400–750 nm with visible laser; full 400–920 nm reflects the combined operational range of the installed unit).
- **Wavelength resolution: 5 nm**; wavelength range variable in **1 nm steps** (continuously tunable, not discrete).
- **Detection width: 10 nm to 320 nm** (continuously variable per channel).
- Maximum pixel size: 8192 × 8192 (galvano); compatible with resonant scanner.
- PMT flexibility: GaAsP / IRGA / GaAs / MA.

### 4.5 DUX-VB4 Filter Cubes

| Filter Cube | Code | Bandpass / Use |
|---|---|---|
| A1-F 452/45 | MHE57011 | 452/45 |
| AX-F 700/75 | MHE57120 | Em Cy5 for DUX-VB4 |

### 4.6 Diascopic (Transmitted) Detector — AX-DUT-MP (MHE60580)

- Transmitted images with 22 mm FOV.
- Excitation laser up to IR; detection up to **920 nm**.
- Second Harmonic Generation (SHG) signal detection possible (with appropriate items).

### 4.7 DM/IR Cut Filter Kit (MHE60450)

- A1-U-DM1300 for inverted stand.

### 4.8 Confocal AX Detector PMTs

| Component | Code | Qty | Description |
|---|---|---|---|
| GaAsP PMT | MHE60220 | 3 | High-sensitivity, low-noise; green–orange range |
| Multi Alkali PMT | MHE60210 | 1 | High-sensitivity, low-noise; blue + red range |

### 4.9 Confocal First Dichroic Mirror

| Component | Code | Description |
|---|---|---|
| Pentaband DM | MXU95086 | AX - DM 405/445/515/561/640; 1st dichroic for AX pentaband configuration |

**Dichroic reflection bands and transmission windows (approximate):**

This pentaband dichroic reflects excitation laser light at the five laser lines and transmits fluorescence emission in the windows between them. Fluorophore emission falling within a reflection notch will be lost — the dichroic will reflect it back toward the laser rather than passing it to the detector. The approximate band structure is:

| Band | Wavelength range (approx.) | Behaviour | Practical note |
|---|---|---|---|
| Notch 1 | ~395–415 nm | **Reflects** (405 nm laser) | — |
| Window 1 | ~415–435 nm | Transmits | DAPI / Hoechst emission passes here |
| Notch 2 | ~435–455 nm | **Reflects** (445 nm laser) | CFP peak emission (~475 nm) is safe but check the blue edge |
| Window 2 | ~455–505 nm | Transmits | CFP, GFP, Alexa Fluor 488 emission passes here |
| Notch 3 | ~505–525 nm | **Reflects** (515 nm laser) | GFP/YFP emission tail may be clipped; verify if using 514 nm excitation |
| Window 3 | ~525–550 nm | Transmits | YFP, Alexa Fluor 532 emission passes here |
| Notch 4 | ~550–575 nm | **Reflects** (561 nm laser) | mCherry excitation tail and TRITC emission peak may overlap |
| Window 4 | ~575–625 nm | Transmits | TRITC, mCherry, Alexa Fluor 568 emission passes here |
| Notch 5 | ~625–655 nm | **Reflects** (640 nm laser) | Cy5 / Alexa Fluor 647 emission blue edge may be clipped |
| Window 5 | >~655 nm | Transmits | Cy5, Alexa Fluor 647, far-red emission passes here |

⚠️ **These edge wavelengths are approximate**, derived from standard pentaband dichroic design for these laser lines. The actual cut-on/cut-off positions of the installed MXU95086 may differ by several nm. For precise fluorophore selection, request the measured transmission spectrum from Nikon (Michelangelo Colavita or FILM staff) or measure it on-site with a spectrometer.

**Fluorophore selection rules of thumb when using the pentaband dichroic:**

- Avoid fluorophores whose emission peak falls within ±10 nm of any laser line (405, 445, 515, 561, 640 nm).
- For the tunable DUX-VB4, set detection windows within the transmission bands listed above.
- When using the NDD for multiphoton imaging, the pentaband dichroic is typically bypassed (NDD sits before the scan head), so these notch restrictions do not apply to NDD-collected signals.
- If a fluorophore's emission straddles a notch, expect signal loss in that spectral region. Switching to a different first dichroic position (the scan head holds 6 dichroic positions) may resolve this if an alternative is installed.

---

## 5. NSPARC Super-Resolution Detector (MHE62100)

- **AX-ISM-MP NSPARC Unit MP**.
- Image Scanning Microscopy (ISM) with IR lasers.
- Resolution improvement up to **100 nm lateral**, **300 nm axial**.
- Extreme low-noise; ideal for dim samples.
- Works with resonant and galvano scanners, up to 22 mm FOV.
- Includes: main unit, electrical boards, cables, optical switching unit, collimator lens, IR cut filter.
- Standard filter positions:
  - Pos 1: Quad band 446/523/600/677 (4-dye sequential imaging).
  - Pos 2: Single BA 450/50 (Ex 405).
  - Pos 3: Single BA 525/50 (Ex 488).
  - Pos 4: Single BA 585/65 (Ex 561).
  - Pos 5: Single BA 700/75 (Ex 640).

### 5.1 NSPARC Additional Filter

| Component | Code | Description |
|---|---|---|
| Triple-band filter | MXU96226 | 445/515/561 nm |

---

## 6. Laser Sources

### 6.1 Multiphoton Laser — Spectra Physics Insight X3+ Dual (1THNEWPC)

| Parameter | Main Output | Dual Output |
|---|---|---|
| Tuning Range | 680–1300 nm | 1045 nm (fixed) |
| Average Power @ 700 nm | > 1.5 W | — |
| Average Power @ 800 nm | > 2.4 W | — |
| Average Power @ 900 nm | > 3.0 W | — |
| Average Power @ 1000 nm | > 2.7 W | > 3.5 W |
| Average Power @ 1100 nm | > 2.4 W | — |
| Average Power @ 1200 nm | > 2.1 W | — |
| Average Power @ 1300 nm | > 1.5 W | — |

### 6.2 Visible Laser Unit — LUA-S6 (MHF49020)

- Six lines: **405 / 445 / 488 / 514 / 561 / 640 nm**.
- Complex Monolithic Optic (CMO) combiner: permanent alignment, maximum throughput, no manual calibration.

### 6.3 IR Optical Path

| Component | Code | Description |
|---|---|---|
| Dual IR Alignment Unit | MHV55530 | Combines main beam (up to 1300 nm) and sub beam (up to 1040 nm); motorised shift mirror + alignment sensor; auto-aligns to AX R MP scan head |
| Incident Optical Unit (Main) | MHE61000 | Motorised focusing for IR pulsed laser up to 1300 nm into scan head |
| Incident Optical Unit (Sub) | MHE61010 | Focusing for 2nd IR pulsed laser up to 1040 nm |

### 6.4 Laser Connection & Safety

| Component | Code | Description |
|---|---|---|
| LUA–AX Connection Kit A | MHF46800 | Connects LUA to AX controller |
| Laser Indicator | MHF49210 | LU-IND; required for LUA-based system |
| Interlock Cable | MXA22194 | IL cable for Ti2 and NI-TT2 heads |
| Interlock Box | MHF49200 | LU-INTL; hub for controllers and interlocking |
| MP Interlock Switch Unit | MHF52000 | A1-MP-TI2S; for multiphoton and N-SIM on Ti2-E |
| Laser Interlock Lid | 1OKH201D | Safety switch on chamber lid; 30 mm glass window; Koehler illumination compatible |

---

## 7. FLIM — PicoQuant 2-Detector System (1PQNEWPC)

- **FLIM, FRET, and FCS** in one turn-key system.
- Customised for Nikon LSMs.
- Up to **8 detection channels**.
- Fluorescence lifetimes: **100 ps to µs**.
- Filters for: CFP, GFP, YFP, DsRed, mCherry, Alexa Fluor 647.
- Software: **SymPhoTime 64** + **NovaFLIM** (4-year licence).
- Includes installation and training.

### 7.1 FLIM Software Integration

| Component | Code | Description |
|---|---|---|
| NIS-A FLIM Module | MXS58000 | Required for confocal + PicoQuant FLIM integration in NIS-Elements |

---

## 8. Cameras

| Camera | Code | Description |
|---|---|---|
| Hamamatsu ORCA-Flash4.0 v3 | 1HMA1444 | USB option; sCMOS |
| Basler MED acA2440-75uc | MXBA0006 | Colour camera |
| USB 3.0 Cable (Basler) | MXBA0016 | MicroB 90° to A, 3 m |
| SMA-BNC Trigger Cable | 1HMATC01 | Trigger cables |
| Basler Trigger Cable | 1BA34087 | GP-I/O 6p/open, 10 m |

---

## 9. Objective Lenses

### 9.1 CFI Plan Apochromat Lambda D Series

| Magnification | Code | NA | WD (mm) | Immersion | Cover Glass | Chromatic Correction | FN | Notes |
|---|---|---|---|---|---|---|---|---|
| 4× | MRD70040 | 0.20 | 20.0 | Air | 0 / 0.17 | 405–850 nm | 25 | Part of 4×/10×/20× set (MRD70PAD); correction collar not required |
| 10× | MRD70170 | 0.45 | 4.0 | Air | 0.17 | 405–850 nm | 25 | Part of 4×/10×/20× set; DIC, POL, DF compatible |
| 20× | MRD70270 | 0.80 | 0.80 | Air | 0.17 | 405–850 nm | 25 | Part of 4×/10×/20× set; DIC, POL compatible |
| 60× Oil | MRD71670 | 1.42 | 0.15 | Oil | 0.17 | 405–850 nm | 25 | Spring loaded; DIC, POL compatible |

### 9.2 CFI Plan Apochromat Lambda S Series (Silicone Immersion)

| Magnification | Code | NA | WD (mm) | Immersion | Cover Glass | Chromatic Correction | FN | Notes |
|---|---|---|---|---|---|---|---|---|
| 25×C Sil | MRD73250 | 1.05 | 0.55 | Silicone oil | 0.17 | 405–950 nm | 25 | Correction collar; part of 25×/40× set (MRD73SIL); refractive index ~1.40 matches live cells |
| 40×C Sil | MRD73400 | 1.25 | 0.30 | Silicone oil | 0.17 | 405–950 nm | 25 | Correction collar; part of 25×/40× set; ideal for deep live-cell / tissue imaging |

### 9.3 CFI Plan Apochromat LWD Lambda S Series (Water Immersion)

| Magnification | Code | NA | WD (mm) | Immersion | Cover Glass | Chromatic Correction | FN | Notes |
|---|---|---|---|---|---|---|---|---|
| 20×C WI | MRD77205 | 0.95 | 0.93 | Water | 0.11–0.23 | 405–950 nm | 25 | Correction collar for cover glass thickness; long WD for thick samples |
| 40×C WI | MRD77410 | 1.15 | 0.60 | Water | 0.15–0.19 | 405–950 nm | 25 | Correction collar; combines high NA with long WD for deep imaging |

### 9.4 Immersion Media

| Item | Code | Description |
|---|---|---|
| Immersion Oil F | MXA22168 | 30 cc; for BF, DF, Phase, DIC, UV/Vis fluorescence, PFS, super-resolution; medium viscosity, weak odour |
| Silicone Oil | 1ME37837 | 250 mL, 500 cSt (Sigma-Aldrich 378380) |

### 9.5 Water Immersion Dispenser (MEV54006)

- Supplies pure water to the objective tip for long-term water immersion.
- Operating environment: +20 °C to +38 °C, ≤ 60 % RH (no condensation), altitude ≤ 2000 m.
- Includes 2 × nozzle assemblies (MEV54006-A002).

---

## 10. Piezo Z Stage

| Component | Code | Description |
|---|---|---|
| Mad City Labs Nano-Z500-N2 | MXMCL004 | Z-axis piezo nanopositioning; 500 µm travel range; closed-loop with Nano-Drive controller; USB control |

---

## 11. Environmental Control

| Component | Code | Description |
|---|---|---|
| BOLD LINE 3 Cage Incubator Bundle | 1OKCAG01 | Premixed gas; compatible with Nikon manual/motorised XY stages and MCL piezo; holders for multiwell plates, 35 mm petri dishes, 1″×3″ chamber slides; additional holders available separately |
| Laser Interlock Lid | 1OKH201D | Lid with safety switch (turns off laser when lifted); 30 mm central glass window; Koehler-compatible |

---

## 12. Controller & Cabling

| Component | Code | Description |
|---|---|---|
| Ti2-E Controller (TI2-CTRE) | MEF55037 | Integrated stage + LAPP controller (except H-TIRF); 4 digital I/O via S-TI2-EXT cable; up to 8 I/O with two cables |
| External Trigger Cable (×2) | MXA22149 | 4 digital I/O per cable; two connect directly to Ti2 controller |
| Daisy Cable L | MXA22147 | Connects filter turret to main body |
| C-Mount Adapter (×2) | MQD42005 | 1× C-Mount TV Adapter A |
| LV-TV Tube Adapter | MBB63435 | — |
| UPS | 1WASMUPS | APC Smart-UPS SMT1000I; 1 kVA / 670 W; 220–230 V AC; 8 × IEC 60320 C13 |
| USB 2.0 Cable A-B | MXF60001 | — |

---

## 13. Workstation & Display

### 13.1 HP Z4 G5 Workstation (MPX12007)

- CPU: Intel Xeon W3-2435, 4.30 GHz, 8 cores.
- RAM: 128 GB (4 × 32 GB) DDR5-4800 ECC.
- GPU: NVIDIA RTX 4000 Ada, 20 GB.
- Storage: 2 TB M.2 SSD (OS) + 2 × 2 TB M.2 SSD (data) + 8 TB HDD 7200 RPM.
- Network: HP 10GBase-T.
- OS: Windows 11 Pro 64 for Workstations.

### 13.2 Monitor

| Component | Code | Description |
|---|---|---|
| HP S7 Pro 734pm | MPX50030 | WQHD, 3440 × 1440 |

---

## 14. Software — NIS-Elements

| Module | Code | Qty | Description |
|---|---|---|---|
| NIS-Elements C-ER | MHS51001 | 1 | Full confocal control: laser/scanner/detector settings, spectral unmixing, 6D imaging, Z-stacks, stitching, multipoint, macro generator, measurement, annotations |
| NIS-Elements AR-SP | MQS31501 | 1 | Passive licence: 3D animations, image analysis (counting, colocalisation, intensity, object metrics), object tracking*, deconvolution*, macro programming, report generator |
| NIS-A General Analysis | MQS43110 | 2 | Processing/analysis for active and passive licences |
| NIS-A Upgrade to GA3 | MQS43150 | 2 | Advanced functions: complex 3D analyses (requires MQS42940), tracking (requires MQS42900/42950), deconvolution (requires MQS42750/42690) |
| NIS-A 2D/3D Deconvolution | MQS42700 | 1 | Blind (Iterative Asymmetric Blind) and non-blind (Iterative Constrained Tikhonov–Müller) deconvolution; PSF from parameters or measured with nanobeads |
| NIS-A JOBS Editor | MQS43130 | 1 | Create/launch JOBS experiments; JOBS explorer access |
| NIS-A JOBS Viewer | — | 1 | Browse, visualise, and review data acquired via JOBS (see §14.1) |
| NIS-A FLIM Module | MXS58000 | 1 | Confocal + PicoQuant FLIM integration |
| NIS.Ai Module | MQS43200 | 1 | AI tools: Enhance.ai, Convert.ai, Segment.ai |

### 14.1 JOBS Ecosystem — Editor, Wizard, and Viewer

The JOBS module is a visual-programming environment for designing automated acquisition and analysis experiments without writing code. It consists of three tightly integrated components:

**JOBS Editor** (MQS43130) — the design surface where experiments are built. Users drag and drop acquisition, analysis, and decision nodes to construct arbitrarily complex workflows. Key capabilities:

- Visual (graphical) programming — no scripting required; nodes are connected by dragging.
- Conditional / intelligent acquisition — General Analysis (GA) results can feed back into acquisition parameters (e.g. re-image only wells that meet a criterion).
- Multi-modality sequencing — chain widefield, confocal, TIRF, SIM, and multiphoton acquisitions within a single experiment.
- High-content screening support — native well-plate, slide, and petri-dish definitions (including custom geometries); 96-well plate imaging achievable in under one minute.
- Object-of-interest acquisition — acquire high-resolution images only at locations where low-magnification pre-scans detected targets.
- On-the-fly analysis — General Analysis pipelines run during acquisition, eliminating post-processing bottlenecks and enabling real-time decision loops.
- Pre-built job templates — NIS-Elements ships with ready-made templates that can be loaded, modified, and saved as new jobs or exported to `.BIN` files.

**JOBS Wizard** — a guided launcher that walks users through experiment parameters (well-plate selection, optical configuration, Z-stack settings, autofocus strategy, labelling) without exposing the full editor, suitable for routine or standardised runs.

**JOBS Viewer** — a dedicated browsing and review interface for data produced by any JOBS run. Features:

- Thumbnail-based navigation across all acquired positions, time points, and channels for rapid visual review.
- Inline display of analysis results (measurements, counts, graphs) generated during or after acquisition.
- Full dataset viewing modes inherited from NIS-Elements core: Volume View (3D rendering), Tile View (time / Z / multipoint), and Slice View (Z / time).
- All images stored in a structured JOBS database, enabling organised retrieval without manual file management.
- Supports review of results from conditional workflows — users can trace which wells or positions triggered re-acquisition or were skipped by decision nodes.

**Workflow relevance for LLM-based experiment design:** The JOBS Editor's node-graph structure maps naturally to a directed acyclic graph (DAG), making it amenable to programmatic generation of experiment definitions. An LLM can reason about available modalities, objective sets, and detector configurations (documented in the preceding sections) to propose JOBS workflows as ordered node sequences with branching logic.

---

## 15. Capability Summary

This system supports the following imaging modalities and workflows:

| Modality | Key Components |
|---|---|
| **Widefield fluorescence** | D-LEDI (4-channel LED), quad-band filter cube, ORCA-Flash4.0 v3 |
| **DIC / Phase contrast** | DIC sliders (20×/40×/60×), analyser cube, intelligent polariser, LWD condenser |
| **Laser-scanning confocal** | AX R scan head (galvano up to 8192²), LUA-S6 six-line VIS laser, DUX-VB4 4-ch descanned detector, GaAsP/MA PMTs |
| **Resonant confocal** | Resonant mirror (up to 2048²), AD-R2K conversion unit |
| **Multiphoton (2P/3P)** | Insight X3+ dual laser (680–1300 nm + 1045 nm fixed), NDD with GaAsP PMTs (up to 4 ch), diascopic detector |
| **Super-resolution (ISM)** | NSPARC unit (100 nm lateral / 300 nm axial), works with galvano and resonant scanners |
| **FLIM / FRET / FCS** | PicoQuant 2-detector system (SymPhoTime 64, NovaFLIM), NIS-A FLIM module, AUX laser port |
| **SHG (Second Harmonic)** | Diascopic detector (AX-DUT-MP), IR laser excitation |
| **Live-cell imaging** | PFS v4 (MP-optimised), BOLD LINE 3 cage incubator, water immersion dispenser, piezo Z stage (500 µm) |
| **Tiling / large-area** | Motorised encoded XY stage (100 nm step), NIS-Elements stitching |
| **AI-assisted analysis** | NIS.Ai (Enhance.ai, Convert.ai, Segment.ai), AI-powered scan-head parameters |

---

## 16. Excitation / Detection Quick-Reference

### 16.1 Available Laser Lines

| Source | Lines (nm) |
|---|---|
| LUA-S6 (VIS) | 405, 445, 488, 514, 561, 640 |
| Insight X3+ Main | 680–1300 (tuneable) |
| Insight X3+ Dual | 1045 (fixed) |

### 16.2 Widefield LED Channels

| Channel | Wavelength (nm) |
|---|---|
| 1 | 385 |
| 2 | 475 |
| 3 | 550 |
| 4 | 621 |

### 16.3 Detector Spectral Coverage

| Detector | Range | Type |
|---|---|---|
| DUX-VB4 (descanned) | 400–920 nm (400–650 with IR / 400–750 with VIS) | Tunable (5 nm resolution, 1 nm steps) + filter wheels; detection width 10–320 nm; GaAsP/IRGA/GaAs/MA selectable |
| NDD Epi (multiphoton) | 400–750 nm (1300 system; filter-defined) | GaAsP PMTs; up to 4 ch |
| DUT-MP (diascopic) | Up to 920 nm | Transmitted; SHG-capable |
| NSPARC (super-res) | Filter-defined (see §5) | ISM detector |
| PicoQuant FLIM | Filter-defined | Up to 8 ch; 100 ps – µs lifetime range |
| ORCA-Flash4.0 v3 | Camera-dependent | sCMOS widefield |
| Basler MED acA2440-75uc | Camera-dependent | Colour; widefield/navigation |

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## 17. Key Specifications at a Glance

| Parameter | Value |
|---|---|
| Z-drive resolution (closed loop) | 20 nm |
| Z-drive resolution (open loop) | 10 nm |
| XY stage travel range | 114 × 73 mm (±57 × ±36.5 mm) |
| XY stage minimal step | 100 nm |
| XY stage repeatability | ±500 nm |
| XY stage speed | 25 mm/s |
| Piezo Z range | 500 µm |
| Confocal max pixel size (galvano) | 8192 × 8192 |
| Confocal max pixel size (resonant) | 2048 × 2048 |
| Galvano max frame rate | 10 fps (512 × 512); 240 fps (512 × 16 band scan) |
| Resonant max frame rate (2K) | 7.5 fps (2048 × 2048); 30 fps (2048 × 512); 720 fps (2048 × 16 band scan) |
| Pinhole range | 6–153 µm |
| Zoom range | 1–1000× continuous |
| Simultaneous channels | 5 (including diascopic) |
| DUX-VB4 wavelength resolution | 5 nm; tunable in 1 nm steps |
| DUX-VB4 detection width | 10–320 nm (continuously variable) |
| NSPARC lateral resolution | ~100 nm |
| NSPARC axial resolution | ~300 nm |
| Scan-head FOV | 22 mm |
| MP laser tuning range | 680–1300 nm |
| MP laser fixed output | 1045 nm |
| FLIM temporal resolution | 100 ps |
| PFS version | v4 (MP-optimised) |
| Objective NA (max, oil) | 1.42 (60× Lambda D Oil) |
| Objective NA (max, water) | 1.15 (40×C WI) |
| Objective NA (max, silicone) | 1.25 (40×C Sil) |

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*Document generated for LLM-assisted workflow design. All pricing, personal identifiers, and contact information have been removed.*