Optical Microscopes | Imaging Methods Core Facility

Carl Zeiss LSM 880 NLO

Inverted confocal microscope
Multiphoton excitation and non-descanned detection with FLIM option
Internal spectral detection unit

Multi-functional fluorescence inverted confocal microscope with single- or multi-photon excitation, internal spectral detection and non-descanned detection with FLIM option.

Applications

Fast and multi-color confocal imaging
Various measurement options: z-stack, time series, tile scan, multi positions and regions
Spectral detection, spectral unmixing and fingerprinting
Deep imaging of thick biological samples with multiphoton excitation and non-descanned detection
Label free imaging: Coherent anti-Stokes Raman Scattering (CARS) and higher harmonic generation (SHG and THG)
FLIM with multiphoton excitation
Long term live-cell imaging available

Specifications

Motorized inverted fluorescence microscope Carl Zeiss Axio Observer.Z1 with confocal module LSM 880 NLO equipped with the following:

Software

ZEN 2.1 Black with following modules and functionalities:
Spectral Unmixing, 3D visualization, Tiles & Positions, FRAP, Experiment designer

Illumination

Transmitted Light Illuminator HAL 100
Epifluorescence Illuminator HXP 120 V
Lasers (CW)

405 nm Laser 30 mW
Argon Laser (458, 488, 514 nm) 25 mW
561 nm Laser 20 mW
633 nm Laser 5 mW

Lasers (pulsed)
- Ti:Sapphire femtosecond laser Chameleon Ultra II (Coherent),
  690-1080 nm, > 3.5W
- Optical parametric oscillator (Chameleon Compact OPO, Coherent),
  1100-1300 nm
- Delay line with LMS-270 precision liner stage (PI) in the Chameleon
  beam path

Detection

2x transmitted light detector LSM T-PMT
Internal spectral detection unit

2 standard PMTs („blue“ and „red“ 371-740 nm)
Spectral detector 32-channels GaAsP PMT (410-695 nm)
Spectral GaAsP detector and „red“ PMT enables photon counting mode

Non-descanned detection unit (reflected geometry)

Spectral detector 32BiG.2 unit (containing 2 detectors)
High Speed Hybrid Detector for TCSPC HPM-100-40 (Becker & Hickl), IRF 120 ps
Range of dichroic beam-splitting filter cubes

Objectives

Objective Type	Immersion	Magnification	N.A.	WD[mm]	DIC/Correct. Ring
EC Plan-Neofluar 420330-9901	Air	5x	0.16	18.5	-
Plan-Apochromat 420640-9900	Air	10x	0.45	2.10	-
LD LCI Plan-Apochromat 420852-9871	Oil, Water, Glycerine	25x	0.8	0.57*	DIC, Corr (CG=0-0.17mm)
C-Apochromat 421867-9970[1]	Water	40x	1.1	0.62*	DIC, Corr (CG=0.14-0.19mm)
C-Apochromat 421787-9970[1]	Water	63x	1.2	0.28*	DIC, Corr (CG=0.14-0.19mm)
Plan-Apochromat 420782-9900[1]	Oil	63x	1.4	0.19	DIC
* at CG = 0.17

Filter Cubes (turret with 6 positions)

Filter set 49 DAPI	EX 365, BS 395, EM 445/50	exchangeable
Filter set 38 GFP	EX 470/40, BS 495, EM 525/50	exchangeable
Filter set 43 Cy3	EX 545/25, BS 570, EM 605/70	exchangeable
	BS-MP 355/690+(R)	fixed position
	BS-MP-760	fixed position
Rear (100% mirror)		fixed position

On request (instead of one of the sets above): Filter set 50 Cy5: EX 640/30, BS 660, EM 690/50

Beam splitters in scanning head

Main beam splitters 1 (visible)	Main beam splitters 2 (invisible)
MBS 458	MBS 405
MBS 458/514	MBS 445
MOBS 458/561	MBS 690+
MBS 488	MBS 760+
MBS 488/561	MBS 405/760+
MBS 488/561/633	MBS 445/760+
MBS T80/R20	MBS T80/R20
Plate	Plate
None	None

Confocal scanning module LSM 880

13 fps for 512x512, zoom 0.6 - 40x, max. resolution 8192 x 8192

FLIM Option

BiG.2 and TCSPC HPM-100-40 non-descanned detectors can be on request attached to a TCSPC card (TimeHarp 260 Nano, PicoQuant)

show less

Nikon CSU-W1

Spinning disk confocal microscope
Dual camera, 7 laser wavelengths
FRAP/Photoactivation module
Heating/cooling stage top incubator

Versatile spinning disk confocal microscope equipped with seven excitation lasers, epifluorescence LED light source, and two back-illuminated sCMOS cameras. The microscope is equipped by stage-top heating/cooling incubator for live cell and tissue imaging and a FRAP/photoactivation module. It is based on an inverted widefield microscope Nikon Eclipse Ti2 equipped with motorized XY stage, Perfect Focus System, semi-motorized DIC, LED transmitted light source, multicolor LED for wide-field epifluorescence, piezo stage for fast z-stack acquisition, and automatic water dispenser for long term imaging.

Applications

Fast multicolor confocal imaging
Various measurement options: z-stack, time series, tile scan, multi positions
Brightfield and DIC microscopy
FRET imaging

Specifications

Software

NIS-Elements

Spinning disk module

Yokogawa CSU-W1

Pinhole size [μm]
(dual disk)

25, 50

Laser excitation wavelengths [nm]
(all CW)

405, 445, 488, 515, 561, 594, 640

Dichroic mirrors (spinning disk module)

quad-band dichroic mirror 405/488/561/638 nm
tripple-band dichroic mirror 445/514/594 nm

Image splitting mirrors (spinning disk module)

561 nm long-pass dichroic mirror (DM A561LP)
514 nm long-pass dichroic mirror (DM A514LP)
empty position for single camera acquisition

Filter cubes (microscope)

DAPI/FITC/TRITC/Cy5
CFP/YFP/mCherry
FITC
TRITC

Emission filters

455/50, 480/40m, 525/50, 545/40, 600/50, 645/75, 690/50, 720/60, 455/50, 480/40, 525/50, 545/40, 440/521/607/700 nm quad-band bandpass filter,
475/543/702 nm triple-band bandpass filter,
Dual Line Emitter 405 / 488

Objectives

Objective Name	Magnitude	Immersion	N.A.	WD[MM]
CFI Plan Apo Lambda 10X	10	air	0.45	4
CFI Plan Apo VC 20x	20	air	0.75	1
CFI Plan Apo Lambda S 25XC Sil	25	silicone oil	1.05	0.55
CF Plan Apo VC 60XC WI	60	water	1.20	0.31-0.28
CFI SR HP Plan Apo Lambda S 100XC Sil	100	silicone oil	1.35	0.31-0.28
CFI Plan Apo VC 100X Oil	100	oil	1.40	0.13

Epifluorescence source

CoolLED pE-4000 (365, 385, 405, 435, 460, 470, 490, 500, 525, 550, 580, 595, 635, 660, 740, and 770 nm)

Tube lenses

1x, 1.5x

Relay lens magnification

1x, 2x, motorized changer

Camera (2x)

PRIME BSI (Teledyne Photometrics)

2048 x 2048 pixels
pixel size: 6.5 x 6.5 μm
63 fps @ 2048 x 2048 pixels, 11-bit data
QEmax> 95%

show less

Abberior Instruments STED – INFINITY

3 dedicated 60x STED objectives (water, oil, and silicone)
5 excitation lines (405, 440, 485, 561, and 640 nm)
Pulsed ultra-high-power STED laser (775 nm)
3 APD-based spectral detection channels
2 Spectral MATRIX detector (APD array) allowing differential detection on two channels
TIMEBOW for measuring fluorescence lifetime with and without super resolution
Adaptive optics for STED beams based on SLM technology
Adaptive optics system (DFM deformable mirror) for all beams (excitation, emission, and depletion)
Full auto-alignment
Continuous hardware autofocus for STED & confocal
Adaptive illumination package for highest resolution and live-cell super-resolution imaging at ultra-low light levels (RESCue,
DyMIN, MINFIELD)

For more detailed microscope characteristics please see the section “Microscope”. Basic introduction to STED microscopy can be found here:

https://abberior-instruments.com/knowledge/microscopy-tutorials/sted/

Specifications

Software	Lightbox Software for Facility Line ImSpector TIMEBOW Software Package for Lightbox
Epifluorescence	CoolLED pE-4000, 16 LEDs
Epifluorescence cubes	FITC TRITC QUAD (DAPI/FITC/Cy3/Cy5)
Excitation lasers	405 nm 440 nm 485 nm 561 nm 640 nm All lasers are pulsed
STED Laser	775 nm (40 MHz pulsed laser, for 2D and 3D STED)
Donut formation	Programmable Spatial Light Modulator – 775 nm
Scanner	Abberior QUAD scanner
Objectives	Olympus/Evident UPLXAPO10X, 10x/NA 0.4 Dry, WD 3.1mm Olympus/Evident UPLXAPO20X, 20x/NA 0.8 Dry, WD 0.6mm Olympus/Evident UPLSAPO30XS, 30x/NA 1.05, silicone oil, WD 0.8mm Olympus/Evident UPLSAPO60XW, 60x/NA 1.2, Water, WD 0.28mm Olympus/Evident UPLSAPO60XS, 60x/NA 1.3, Silicone Oil, WD 0.3mm Olympus/Evident UPLXAPO60XO, 60x/NA 1.42, Oil, WD 0.15mm
Rainbow Spectral Detection Kit	Low-loss, background-free, variable spectral detection Detection bands fully tunable between 400 and 800nm No dispersive elements required Fully integrated in Lightbox software, detection bands can be selected at an instant
Pinholes	16 pinholes from 25 μm to 2 mm
Detectors	3x Single-photon-counting APD with a superior sensitivity (up to 65% photon detection efficiency) 2x MATRIX detector (consist of multiple avalanche photo diodes with quantum efficiency over 50 % at 500 nm in a hexagonal arrangement on a single detector chip, allows pixel re-assignment and differential detection)
FLIM	Time Correlated single photon counting hardware (High-Throughput Multichannel Event Timer & TCSPC Unit: MultiHarp 150) Simultaneous multi color lifetime recording (up to 2 FLIM APD detection channels) Synchronization unit between Picoquant and Abberior Instruments hardware On-the-fly lifetime analysis of every single photon detector
RAYSHAPE Adaptive Optics system	Deformable mirror-based correction of arbitrary aberrations for all beams More than 140 elements with a stroke of several microns ensure precise correction, even of high-order aberrations Compensates for sample-induced aberrations, e.g. when focusing into a refractive-index mismatched sample, or into samples with internal inhomogeneities Applied spherical correction changes with focus to ensure automatic correction at all focal depths No moving elements in the objective Enables superior signal and resolution, in particular with 3DSTED, but also for confocal and multiphoton images, e.g. of thick tissue samples
FLEXPOSURE Adaptive Illumination	Light dose minimization by up to two orders of magnitude to leverage live cell imaging Bleaching reduction applicable to all fluorescent markers Based on concurrent, pixel-wise decision-making of whether structure is present in the current pixel RESCue, DyMIN, MINFIELD, see https://abberior.rocks/superresolution-confocal-systems/modules/flexposure-illumination/

Abberior Instruments STED

Inverted confocal microscope
STED super-resolution microscopy

Fluorescence inverted confocal microscope and STED super-resolution nanoscope with high detection efficiency of far-red photons. The system is equipped with four excitation lasers, depletion laser 775 nm and four single photon counting detectors. For more detailed microscope characteristics please see the section “Microscope”. Basic introduction to STED microscopy can be found here:

https://abberior-instruments.com/knowledge/microscopy-tutorials/sted/

Applications

Two-color 2D and 3D super-resolution images obtained by STED technique with a pulsed depletion laser 775 nm and pulsed excitation 561 nm and 640 nm
STED RESCUE and DYMIN mode available (STED imaging mode that significantly reduces the light dose sent onto the sample without compromising the resolution)
2D and 3D STED images available also with water immersion objective
Multicolor confocal scanning system with variable pinhole size
Possible FLIM or FCS acquisition
Live cell imaging
NIR confocal imaging (775 nm excitation)

Specifications

Inverted confocal microscope Nikon Eclipse Ti-E equipped with a piezo Z-stage, motorized XY stage, Perfect Focus System, transmitted light lamp (100 W) and following units:

Software	Imspector (v16.3)
Epifluorescence	CoolLED pE-4000
Epifluorescence cubes	FITC (465-495, DM505, 515-555) TRITC (527-553, DM565, 577-633) QUAD (DAPI/FITC/Cy3/Cy5) Analyzer
Excitation lasers	cw - 405 nm, pulsed - 485 nm, 561 nm, 640 nm, and 775 nm
STED Laser	775 nm (40 MHz pulsed laser, for 2D and 3D STED)
Donut formation	Programmable Spatial Light Modulator – 775 nm
Scanner	Abberior QUAD scanner: line frequency up to 2.5 kHz
Objectives	Nikon CFI Plan Apo Lambda 60x Oil, NA 1.40, WD 0.13 mm Nikon CFI Plan Apo 60x WI, NA 1.27, WD 0.17 mm, Correction Collar 0.15-0.19, DIC Nikon CFI Plan Apo Lambda 10x, NA 0.45, WD 4 mm, DIC
Emission filters	422-467 nm 506-594 nm (or 500-550 nm) 580-630 nm 650-720 nm (or 800-870 nm)
Pinholes	16 pinholes from 25 μm to 2 mm
Detectors	4x Photon Counting Module (Excelitas Technologies) Two time resolved detectors optimized for FLIM High detection sensitivity for red light (>62% for 680nm) PMT for transmitted and reflected light (Hamamatsu Photonics) Monochrome widefield camera DMK 23U274 (Imaging Source) CCD sensor, 1600×1200 (1.9 MP), up to 20 fps, pixel size 4.4 µm x 4.4 µm
FLIM	Externally connected TCSPC card: TimeHarp260N (PicoQuant) Two independent channels, ultra-short dead time <2ns, temporal resolution 250 ps

show less

Carl Zeiss Lattice Lightsheet 7

Short term, long term live cell imaging at subcellular resolution
Low phototoxicity and photobleching
Dual camera setup for colocalization studies
High speed volumetric imaging, penetration depth up to 200 µm
Tissue culture cells, cells in hydrogel up to spheroids and organoids

Lightsheet microscope with gentle light sheet imaging at high resolution and volumetric speed with standard sample carriers. Complex alignment processes are performed automatically on workstation with high-speed data transport connection.

Applications

Volumetric live cell imaging of:

- adherent or suspension cells
- 3D cell cultures: cysts, cells in hydrogel, organoids, spheroids with diameter up to 200µm
- Small evolving organisms: zebrafish embryo, C.elegans embryo, Drosophila embryo

Specifications

Software	ZEN 3.6 (blue edition)
Illumination	LED (white & red) for transmitted lightE Laser (488 nm, 561nm, 640 nm) for beam adjustment and fluorescence imaging
Cameras	2x Hamamatsu Orca-Fusion sCMOS camera
Objectives	Illumination: 13.3x/ NA 0.4 Detection: 44.83x / NA 1.0
Filters	Emission Filter Camera 1 BP 570-620 + LP 655 BP 495-550 + LP 655 LBF 405/488/561/642 ND filter Empty BP 495-570 LP 570 Emission Filter Camera 2 BP 570-610 IR+ Empty BP 495-550 + BP 570-620 BP 500-550 IR+ Secondary Beam Splitter Plate LP 565 LP 640 Empty
Resolution	Deskewed: 330 nm × 330 nm × 500 – 1000 nm; Deskewed w/DCV: 290 nm × 290 nm × 450 nm– 900 nm (z-res. = light sheet thickness if ≤1000 nm)
Light sheets	Beam shaping by cylinder lens and spatial light modulator (SLM) Pre-defined Sinc3 beams with length [μm] × thickness [nm]: 15 × 550 (w/side lobes) & 15 × 650 (w/o side lobes) 30 × 700 (w/side lobes) & 30 × 1,000 (w/o side lobes) 100 × 1,400 (w/side lobes) & 100 × 1,800 (w/o side lobes)
Acquisition rate	Volume: 3 Vol/s @ approx. 300 μm × 50 μm × 20 μm Plane: 400 frames/s @ approx. 300 μm × 20 μm
Sample carrier frames	"Dish 35": for 35 mm cell culture dishes "Dish 35...40": for 35 – 40 mm cell culture dishes "Slide": for slides 26 mm × 76 mm; also suitable for multi-well glass-bottom slides 26 mm × 76 mm "Chamber slide": for LabTekR chambers 25 mm × 57 mm; also suitable for multi-well glass-bottom slides 25 mm × 57 mm "Multiwell": for multiwell microplates 85.48 mm × 127.76 mm
Environmental control	Heating system, gas mixer system (CO2 and N2 level control) - integrated in the software

show less

Nikon iLas 2 ring-TIRF/FRAP

Inverted widefield microscope
ring-TIRF illumination
Image splitter (optional)
Two cameras (sCMOS, EM-CCD)

Inverted fluorescence widefield microscope based on Nikon ECLIPSE Ti2 microscope body and iLas 2 (Gataca Systems) illumination device allowing ring-TIRF microscopy and FRAP.

Applications

Fast multicolor widefield imaging with TIRF or HILO excitation option
Bright-field microscopy
Epi-fluorescence
Interference reflection microscopy
FRAP (fluorescence recovery after photobleaching) measurements
Option of simultaneous dual wavelength imaging by single camera
Long term live-cell imaging available

Specifications

Inverted widefield microscope body Nikon Eclipse Ti2, motorized XY stage, Perfect Focus System, automatized H-TIRF module, insertable gradation neutral density filter, transmitted light lamp (100 W) and following units:

Software	NIS-Elements
Epifluorecence	CoolLED pE-300, 400 nm, 460 nm, 550 nm
Laser excitation wavelengths	405 nm, 488 nm, 561 nm, 640 nm (all cw)
Objectives	Nikon Plan Apo λ 20x, NA 0.75, WD 1.00 mm Nikon Apo TIRF 60x Oil, NA 1.49, WD 0.12 mm, Correction Collar 0.15-0.19, DIC
Filter cubes	Chroma TRF89901v2 ET - 405/488/561/640nm Laser Quad Band Set for TIRF applications TIRF LF488/LP-C Filtrblok TIRF LF561/LP-C Filtrblok Epi-Fl C-FL-HQ Filtrblok F21-020 50R/50T Beamsplitter 400-1000 LED-DA/FI/TR/Cy5-B Filter Cube
Filter turret	465/30 nm BrightLine single-band bandpas 525/45 nm BrightLine single-band bandpas 600/37 nm BrightLine single-band bandpas 697/58 nm BrightLine single-band bandpas
Tube lenses	1x, 1.5x
Camera	PRIME BSI (Teledyne Photometrics) 2048 x 2048 pixels pixel size: 6.5 x 6.5 μm 63 fps @ 2048 x 2048 pixels, 11-bit data QEmax> 95%

show less

Nikon N-SIM & N-STORM

Inverted widefield microscope
TIRF illumination
Image splitter

Multifunctional fluorescence inverted widefield microscope enabling live-cell imaging, TIRF or HILO illumination and two super-resolution techniques: structured illumination microscopy and single molecule localization microscopy. For more detailed microscope characteristics please see the section “Specification”. Basic introduction to super-resolution microscopy can be found here:

http://zeiss-campus.magnet.fsu.edu/articles/superresolution/introduction.html

Applications

Multicolor (up to 3 colors) super-resolution images obtained by 3D-SIM technique reaching up to 2x better lateral and axial resolution compared to standard widefield imaging
Super-resolution 2D images at high speed captured by „TIRF-SIM“ mode for excitation wavelengths 488 and 561 nm for better understanding of molecular interactions at the cell surface
Two-color super-resolution images obtained by single molecule localization methods (STORM, dSTORM, PALM; TIRF or HILO illumination available) with resolution improvement up to 10x compared to conventional optical microscopes
Fast and sensitive multicolor widefield imaging with TIRF or HILO excitation option
Option of simultaneous dual wavelength imaging by single camera
Long term live-cell imaging available
Brightfield microscopy

Specifications

Inverted widefield microscope Nikon Eclipse Ti-E equipped with a piezo Z-stage, motorized XY stage, Perfect Focus System, automatized H-TIRF module, insertable quarter-wave plate, insertable gradation neutral density filter, transmitted light lamp (100 W) and following units:

Software	NIS-Elements (v5.21)
Epifluorecence	Nikon Intensilight E
Laser excitation wavelengths	405 nm, 445nm, 488 nm, 561 nm, 647 nm (all cw)
Objectives	Nikon CFI HP Apo TIRF 100x Oil, NA 1.49, WD 0.12 mm, Temperature Correction Ring 23-37°C (for STORM) Nikon CFI SR Apo TIRF 100x Oil, NA 1.49, WD 0.12 mm, Temperature Correction Ring 23-37°C (for SIM) Nikon CFI Plan Apo 60x WI, NA 1.27, WD 0.17 mm, Correction Collar 0.15-0.19 (for SIM) Nikon CFI Plan Apo Lambda 20x, NA 0.75, WD 1mm
Cameras	EM CCD Andor iXon Ultra DU897 (Andor Technologies) right port available for both SIM and localization super-resolution techniques, live-cell imaging and TIRF imaging 512x512 pixels pixel size: 16x16 μm frame rate 56 fps for 512x512 pixels, standard mode frame rate up to 1 fps for 512x512 pixels, 3D-SIM acquisition frame rate up to 1.6 fps for 512x512 pixels, TIRF-SIM acquisition sCMOS Hamamatsu ORCA 4.0 V2 (Hamamatsu Photonics) left port available for both localization super-resolution techniques, live-cell imaging and TIRF imaging 2048x2048 pixels pixel size: 6.5x6.5 μm frame rate 100 fps for 2048x2048 pixels, standard scan
Filter turret 1	DAPI (361-389, DM415, 430-490) CFP TIRF (436/20, 442rdc, 460lp, 480/40) – inserted on demand 488 TIRF (488/10, 488rdc, 500lp, 525/50) 561 TIRF (561/10, 561rdc, 575lp, 600/50) Cy5 (628/40, DM660, 731/137) – inserted on demand continuous STORM TIRF (excitation, mirror, emission: 387-417, 420-481, 422-478 483-494, 497-553, 502-549 557-570, 575-628, 581-625 636-661, 667-792, 674-786) HM Half Mirror
Filter turret 2	SIM488 (470-490, DM515, 500-545) SIM561 (556-566, DM590, 570-640) SIM647 (590-650, DM665, 663-738) HM Half Mirror
Tube lenses	1x, 1.5x
Relay lenses in front of ORCA Camera	1x (widefield), 0.4x (STORM)
Relay lenses in front of EM CCD Camera	1x (astigmatism lens for STORM) 1x (widefield) 2.5x (SIM)
Astigmatism lens (for 3D STORM)	Yes, insertion possible for both cameras
SIM diffraction grating blocks	3D EX V-R (3D-SIM 100x oil objective) 3D EX V-R (3D-SIM 60x water objective) TIRF 488 (TIRF 100x oil objective) TIRF 561 (TIRF 100x oil objective)
Image splitter	DV2 (Photometrics) inserted on demand available beamsplitters: 565 nm (T565lpxr), 505 nm (T505lpxr), Polarization/Anisotropy module W-VIEW GEMINI (Hamamatsu Photonics) inserted on demand available beamsplitters for 484 nm, 560 nm, 640 nm, and 700 nm

show less

Nikon Ti-E H-TIRF

Inverted widefield microscope
TIRF illumination
Image splitter

Versatile fluorescence inverted widefield microscope equipped with four lasers, epifluorescence lamp and EM-CCD and CMOS cameras. The microscope is designed for short and long live-cell imaging and experiments under standard or TIRF illumination. Link to manufacturer website:

https://www.nikoninstruments.com/cz_CZ/Vyrobky/Inverzni-mikroskopy/Eclipse-Ti-E

Applications

Fast and sensitive multicolor widefield imaging with TIRF, HILO or EPI excitation option
Option of simultaneous dual wavelength imaging by single camera
Short or long term live-cell imaging available
Various measurement options: z-stack, time series, tile scan, multi positions
Brightfield and DIC microscopy

Specifications

Inverted widefield microscope Nikon Eclipse Ti-E equipped with motorized XY stage, Perfect Focus System, H-TIRF module, module for environmental control Okolab (temperature controlled range room temperature up to 40°C; CO2 0-10%; humidity up to 95 %), insertable quarter-wave plate, insertable gradation neutral density filter, transmitted light lamp (100 W) and following units:

Software	NIS-Elements Ar (v5.02)
Epifluorecence	Nikon Intensilight E
Laser excitation wavelengths	405 nm, 488 nm, 561 nm, 640 nm (all cw)
Objectives	Nikon CFI Apo TIRF 60x Oil, NA 1.49, WD 0.12 mm, Correction Collar, DIC (motorized prism insertion) Nikon CFI Plan Apo 60x WI, NA 1.27, WD 0.17 mm, Correction Collar 0.15-0.19, DIC Nikon CFI Plan Apo Lambda 20x, NA 0.75, WD 1mm, DIC Nikon CFI Plan Apo Lambda 10x, NA 0.45, WD 4 mm
Cameras	EM CCD Andor iXon Ultra DU888 (Andor Technologies) right port 1024 x 1024 pixels pixel size: 13 μm x 13 μm 26 fps at 1024 x 1024 pixels, QEmax> 90% PRIME BSI (Teledyne Photometrics) 2048 x 2048 pixels pixel size: 6.5 x 6.5 μm 63 fps @ 2048 x 2048 pixels, 11-bit data QEmax> 95%
Filter turret	TagBFP (excitation 395-415, emission 435-485) EGFP (483-493, 500-550) mCherry (556-566, 593-668) Cy5 (632-652, 669-741) Quad Band Set - 405/488/561/640
Tube lenses	1x, 1.5x
Image splitter	W-View Gemini (Hamamatsu Photonics) in front of Hamamatsu camera available beamsplitters: 484 nm, 560 nm, 640 nm and 700 nm

show less

Nikon Ti-E H-TIRF 2

Inverted widefield microscope
TIRF illumination

Versatile fluorescence inverted widefield microscope equipped with three lasers, epifluorescence lamp, and back-illuminated sCMOS camera. The microscope is designed for short- and long-term imaging experiments under standard or TIRF illumination. Links to manufacturer website:

https://www.microscope.healthcare.nikon.com/products/inverted-microscopes/eclipse-ti2-series

Applications

Fast and sensitive multicolor widefield imaging with TIRF, HILO or EPI excitation option
Various measurement options: z-stack, time series, tile scan, multi positions
Brightfield and DIC microscopy

Specifications

Inverted widefield microscope Nikon Eclipse Ti2 equipped with motorized XY stage, Perfect Focus System, H-TIRF module, insertable quarter-wave plate, insertable gradation neutral density filter, transmitted light lamp (Nikon TI2-D-LHLED) and following units:

Software	NIS-Elements AR (v. 5.20)
Epifluorecence	CoolLED pE-300, 400 nm, 460 nm, 550 nm
Laser excitation wavelengths	488 nm, 561 nm, 640 nm (all cw)
Filter turret	EM435-485 EM500-545 EM610/75 EM700/75 Quad Band Set - 405/488/561/640
Objectives	Nikon Plan Apo λ 20x, NA 0.75, WD 1.00 mm Nikon Apo TIRF 60x Oil, NA 1.49, WD 0.12 mm, Correction Collar 0.15-0.19, DIC
Tube lenses	1x, 1.5x
Relay lens (mountable)	2.5x
Camera	PRIME BSI (Teledyne Photometrics) 2048 x 2048 pixels pixel size: 6.5 x 6.5 μm 63 fps @ 2048 x 2048 pixels, 11-bit data QEmax> 95%

show less

Leica TCS SP8 WLL SMD-FLIM

Inverted confocal microscope
WLL and internal spectral detection unit
FLIM and FCS

Versatile inverted fluorescence confocal microscope equipped with 405 nm, 445 nm and white light laser, spectrally tunable detection and FLIM hardware. Presence of camera and epifluorescence lamp allows also widefield imaging. For more detailed microscope characteristics please see the section “Specifications”.

Applications

Multi-color confocal imaging
Multi-color widefield imaging
Various measurement options: z-stack, time series, tile scan, multi positions
Spectral imaging
Measurement of emission and excitation spectra
Lifetime imaging, FLIM-FRET
Measurement of e.g. membrane dynamics by FCS and FRAP
Live-cell imaging available: stage-top incubator with controlled humidity and atmosphere (CO₂+N₂)
Brightfield, DIC, polarized light microscopy

Specifications

An inverted confocal microscope Dmi8 with a laser scanning confocal head Leica TCS SP8, a motorized microscope stage with a Super Z-galvo scanning insert for fast and precise Z movement, HW autofocus and Best focus control, transmitted light LED U-12V, square pinhole of tunable size and following units:

Software

LAS-X

Epifluorescence

CoolLED pE-300

Lasers

405 nm(max 40 MHz, 3 mW)
445 nm(max 40 MHz)
WLL 470-670 nm (max 80 MHz, 1.5 mW)

laser wavelength and intensity is controlled by a combination of AOTF and AOBS
the actual wavelength selectable with 1 nm step
up to 8 parallel laser lines

Additional beamsplitters

BP 440/40

Filter turret (filter cubes for epifluorescence lamp)

DAPI	EX 325-375, BS 400, EM 435-485
FITC	EX 460-500, BS 505, EM 512-542
RHOD	EX 541-551, BS 560, EM 565-605
CY5	EX 590-650, BS 660, EM 662-738

Analyser

Objectives

Objective Type	Magnification	Immersion	N.A.	WD[mm]	DIC/Correct. Ring
HC PL FLUOTAR 1.6x	1.6x	Dry	0.05	1.54	-
HC PL APO CS 10x	10x	Dry	0.40	2.20	-
HC PL APO CS2 20x	20x	Dry	0.75	0.62	DIC
HC PL APO CS2 63x WI	63x	Water	1.20	0.30	DIC, motorized correction collar
HC PL APO CS2 63x Oil	63x	Oil	1.40	0.14	DIC

Scanner

FOV SP8 scanner

maximal sampling 8192x8192px
speed 1-1800 Hz (7fps@512x512 px)
hardware zoom 0.75x-48x

Fluorifier Disc Settings (notch filters)

Turret 1	Turret 2
NF 488	NF 445
NF 514	NF 594
NF 458/514	NF 445/594
NF 488/561/633	SMD1 NF 405/470
MBS 488/561	SMD2 NF 405/640
MBS 488/561/633	SMD3 NF 470/640

Detection

Transmitted light detector (PMT)
Internal spectrally tunable detection unit

3x HyD detectors for FLIM (time-gating possible), GaAsP, 400 – 720 nm, modes: Standard, Counting, BrightR; QE=45%@500nm
2x PMT detectors,400-800nm, QE=30%@500nm

Camera DFC365 FX (Leica)

1392 x 1040 pixels
6.45 μm x 6.45 μm
CCD sensor Sony ICX285
C-mount 0.7x

FLIM and FCS module

HydraHarp400 (Picoquant)

Picosecond Event Timer & TCSPC Module
Four channels available
Enables detection of photon arrival times with respect to the beginning of the experiment, the excitation pulse and the channel in which the photon was registered (TTTR mode). In combination with a scanner controller, a histogram acquisition at different image positions is available.

Symphotime64

Software for image acquisition and analysis

Custom written software in LabView for image acquisition and data analysis.

Navigator module

LAS-X Navigator - software module for quick navigation in the sample and automated stage experiments

Live cell imaging

OKOlab incubation system - regulation of temperature and CO2 and N2 level

show less

Leica TCS SP8 DM6 CFS

Upright confocal microscope
Internal spectral detection unit

An upright fluorescence confocal microscope equipped with four excitation lasers, dipping objectives with long working distance, oil immersion objective and 1x HyD detector and 2x PMTs. Presence of camera, epifluorescence lamp and removable infrared filter allows also widefield imaging in infrared area. Accessory for electrophysiological experiments is also available. For more detailed microscope characteristics please see the section “Specifications”.

Applications

Fast and multi-color confocal imaging
Fast and multi-color widefield imaging
Various measurement options: z-stack, time series
Spectral imaging, measurement of emission spectrum
Option of infrared detection in widefield imaging
Brightfield and polarized light microscopy

Specifications

An upright confocal microscope DM6 CFS with a laser scanning confocal head Leica TCS SP8, a manual microscope stage, Best focus control, transmitted light LED U-12V, removable infrared filter, square pinhole of tunable size and following units:

Software	LAS-X
Epifluorescence lamp	Leica EL6000
Lasers	405, 488, 552, 638 nm (all cw)
Beamsplitters	DD 488/552 TD 488/552/638 RT 15/85
Filter turret – filter cubes for epifluorescence lamp	DAPI (Ex: 325-375; DM: 400; Em: 435-485) FITC (Ex: 460-500; DM: 505; Em: 512-542) RHOD (Ex: 541-551; DM: 560; Em: 565-605) CY5 (Ex: 590-650; DM: 660; Em: 662-738) – not inserted Analyser
Objectives	HC APO L 10x (W), NA 0.30, WD 3.7 mm, dipping objective HC FLUOTAR L 25x (W), NA 0.95, WD 2.5 mm, dipping objective HC PL APO CS2 63x Oil, NA 1.40, WD 0.14 mm Two objectives are installed at maximum.
Scanner	FOV SP8 scanner maximal sampling 8192 x 8192 px speed 1-1800 Hz (7fps@512 x 512 px) hardware zoom 0.75x-48x
Detection	Transmitted light detector (PMT) Internal spectrally tunable detection unit 1x HyD detectors (GaAsP, 400 – 720 nm, Modes: Standard, Counting, BrightR), QE=45%@500nm 2x PMT detectors (400-800nm), QE=30%@500nm Camera DFC365 FX (Leica) 1392 x 1040 pixels 6.45 μm x 6.45 μm CCD sensor Sony ICX285 C-mount 0.7x

show less

Leica DMi8 WF

Inverted widefield microscope

Inverted widefield fluorescence microscope equipped with epifluorescence lamp and EM-CCD camera.

Applications

Fast and multi-color widefield imaging
Various measurement options: z-stack, time series, tile scan, multi positions
Brightfield and DIC microscopy

Specifications

An inverted widefield microscope Dmi8 with motorized microscope stage, transmitted light LED U-12V, and following units:

Software	LAS-X, Navigator
Epifluorescence lamp	CoolLED pE-300
Filter turret	DAPI (Ex: 325-375; DM: 400; Em: 435-485) FITC (Ex: 460-500; DM: 505; Em: 512-542) RHOD (Ex: 541-551; DM: 560; Em: 565-605) CY5 (Ex: 590-650; DM: 660; Em: 662-738) Analyser
Objectives	HC PL FLUOTAR 10x, NA 0.30, WD 11 mm HC PL FLUOTAR L 20x, NA 0.40, WD 6.9 mm HC PL FLUOTAR L 40x, NA 0.60, WD 3.3 mm HC PL APO 63x Oil, NA 1.4, WD 0.14 mm, DIC
Camera: left port	ORCA-Flash4.0 V3 (Hamamatsu) monochrome digital sCMOS camera 2048 x 2048 pixels pixel size: 6.5x6.5 μm readout rate 40 fps for 16bit full frame
Camera: right port	K3C (Leica) color digital CMOS camera 3072 x 2048 pixels pixel size: 2.4 x 2.4 μm bit depth: 3x12bit RGB readout rate 15 fps

show less

Carl Zeiss Axiozoom.V16

Upright macroscope

Fluorescence zoom upright microscope which combines the benefits of stereomicroscopes such as zoom optics and long working distances with the higher resolutions of traditional light microscopes. The macroscope in IMCF at BIOCEV is equipped with a 2.3x magnification objective combined with numerical aperture 0.57 what offers superior brightness in large objects fields. In comparable image fields, the Axio Zoom.V16 offers a 2.5 times higher resolution and 10 times brighter fluorescence than generally used stereomicroscopes. See the product web page.

Applications

visualization of large samples, e.g. whole model organism, in fluorescence contrast or transmitted light with the possibility to zoom in to the smallest details of the sample. Long working distance of the available objectives allows comfortable manipulation with specimens.
basic documentation of histological samples.

Specifications

Axiozoom.V16 is a fluorescence zoom upright microscope equipped with a motorized stage with travel range 150 x 100 mm and the following:

Software

ZEN blue pro 2012

Illumination

Transmitted light – Zeiss CL 9000 LED CAN with day-light filter for cold light LED
Fluorescence - HXP 120 V (D) – long-life, metal halide illuminator

Filter cubes

Filter set 49 DAPI    (Ex: 365; DM: 395; Em: 445/450)
Filter set 38 GFP      (Ex: 470/40; DM: 495; Em: 525/550)
Filter set 63 RFP      (Ex: 572/25; DM: 590; Em: 629/62)
Filter set 50 CY5      (Ex: 640/30; DM: 660; Em: 690/50)

All filter sets are exchangeable.

Objectives

Objective Type	Immersion	Magnification	N.A.	WD[mm]	DIC/Correct. Ring
PlanNeoFluar Z	Air	1x	0.25	56	-
PlanNeoFluar Z	Air	2.3x	0.57	10.6	-

Detection

Camera Axiocam 506 mono

6 Mpix (2752x2208)
pixel size 4,54 μm x 4.54 μm
19 fps at full frame
effective sensor size 12.5 x 10.0 mm

show less

Akoya PhenoCycler-Fusion 2.0

PhenoCycler-Fusion 2.0 enables to detect protein expression on tissues in real time. The system introduces up to 64 cycles automation with rapid fluidics establishing itself as the fastest spatial biology solution enabling to detect up to 100+ biomarkers (3 markers per run plus DAPI as reference). It is a part of an integrated end-to-end workflow containing pre-optimized antibodies and reagents, fast fluidics and imaging, as well as onboard data processing generating high-resolution QPTIFF files. The system features imaging of 1 million cells in 10 minutes by the detection of biomarkers while preserving tissue integrity using barcoding technology. The system allows to stain the tissue also with non-inventoried antibodies conjugated with barcodes via kit. Panel could be built up from an extensive database of antibodies, in-house conjugated antibodies or Akoya offers ready to-use PhenoCode™ Discovery Panels

Features

For FFPE and FF tissue sections, tissue microchips, tissue sections, organoids
Up to 100+ biomarkers on one section by unique barcoding technology
Up to 300+ catalog antibodies or in-house conjugated antibodies
Cell phenotyping
Cellular neighborhood analysis
Slide scanning without multiplexing, brightfield, and fluorescence
25 min of acquisition for 4 colors, at 15 mm x 15 mm, at 20x
QPTIFF file format compatible with Enable Medicine, Visiopharm, QuPath etc.

Specifications

Channels	Opal 7-color DAPI AF488 ATTO 550 Cy5 AF750 Brightfield
Magnification	10x (NA 0.4) 20x (NA 0.7) 40x (NA 0.8)
Resolution	10x (1.0 µm/pixel) 20x (0.5 µm/pixel) 40x (0.25 µm/pixel)
Scanning area	18mm x 35mm
Number of slides processed simultaneously	2 (multiple tissue sections per slide)
Software	PhenoCycler-Fusion 2.3.1. PhenoCycler Experiment Designer 2.1.0. Phenochart 2.2.0. QuPath

show less

Nanolive CX-A

3D holotomography & fluorescence
Stage-top incubator for long-term automatic live cell imaging

Automated holotomographic and fluorescence microscope for long-term live-cell imaging. Label-free 3D imaging of cells in real time is ensured due to the low power laser and top stage. In addition, presence of epifluorescence lamp allows correlative holographic and fluorescence imaging. Link to manufacturer website:

https://www.nanolive.ch/products/3d-microscopes/cx-a/

Applications

Gentle long-term live-cell label-free 3D imaging
Correlative holographic (3D) and fluorescence (2D) imaging
Imaging of cell populations, single cells or organelles
Measurement of refractive indices inside the cell

Specifications

Software	EVE - data acquisition STEVE - data visualization and post-processing
Illumination	520 nm (Class 1 laser low power, sample exposure 0.2 mW/mm2)
Epifluorescence lamp	CoolLED pE-300
Excitation filters	392/23, 474/27, 554/23 or 635/18
Emission filters	For DAPI, FITC, TRITC/Cy5 imaging (Semrock FF01-432/515/595/730)
Objective	Dry objective 60x, NA 0,8
Camera	USB 3.0 CMOS Sony IMX174 sensor Quantum Efficiency 70 % (at 545 nm) Dark Noise 6,6 e¯ Dynamic Range 73,7 dB
Module for environmental control	Tokaihit stage top incubator CO2 concentration range: 5% - 20% (±0.1%) Humidity: ~ 95% Sample temperature: 30-40°C (±0.3°C)
Sample insert	4 dish format 96 well plate
Recommended labware	35 mm low IBIDI dish Cat.No: 80136; optional DIC lid Cat.No: 80050; recommendations: respect dish volume (1-2 ml), use same volume in each well, assure no meniscus, assure no bubbles, change medium before imaging) Nanolive 96-well format plates – recommendations: respect well volume (80-90μl), each well must have the same volume

show less

ImageXpress Micro XLS

cytometry & fluorescence

Fully automated imaging cytometer designed for fast acquisition and analysis of robust data volume by advanced methods of multiparametric cytometric analysis, reconstruction and multidimensional visualization. Link to manufacturer website:

https://www.moleculardevices.com/systems/high-content-imaging/imagexpress-micro-xls-widefield-high-content-analysis-system

Applications

localization, quantification and functional analysis of mitochondria in cell, effectivity and dynamics of internalization of surface structures, viability and morphology of cells or subcellular structures
cytotoxicity, apoptosis/necrosis
cell cycle and mitosis
cell differentiation, number, viability and phosphorylation of cells or subcellular structures, activation/inhibition of signal pathways and phosphorylation of proteins, effectivity of transfection, cell migration and analysis of objects movement
effectivity and dynamics of internalization of surface structures, localization and co-localization of proteins in nuclear, perinuclear, cytoplasmic or membrane localization

Specifications

Automatic hardware autofocus via IR laser. Automatic software autofocus.

Software	1 offline licence Modules: Granularity Application Module Live/Dead Application Module Cell cycle Application Module Multiwavelenght Cell Scoring Application Module Multiwavelenght Translocation Application Module
Epifluorecence	solid state with spectral range 400-640nm and 10 000 hours life time
Objectives	10x Plan Fluor, NA 0.3 20x Ph1 S Plan Fluor ELWD ADM, NA 0.45, appropriate for phase contrast 40x Ph2 S Plan Fluor ELWD ADM, NA 0.60, appropriate for phase contrast
Filters	DAPI eGFP/FITC TRITC
Detector	SCMOS 4.5 MPx, 80-200 frames per sec., 16bit A/D converter, dynamic range 1:20000, low electronic noise 1.4 e/px
Stage	inserts for multiwall plates (6 well – 1536 well) microscopic slides (possible up to 3 slides simultaneously) adjustable in X, Y, Z with 100nm accuracy

show less

Software

Illumination

Detection

Objectives

Filter Cubes (turret with 6 positions)

Beam splitters in scanning head

Confocal scanning module LSM 880

FLIM Option

Software

Spinning disk module

Pinhole size [μm] (dual disk)

Laser excitation wavelengths [nm] (all CW)

Dichroic mirrors (spinning disk module)

Image splitting mirrors (spinning disk module)

Filter cubes (microscope)

Emission filters

Objectives

Epifluorescence source

Tube lenses

Relay lens magnification

Camera (2x)

Software

Epifluorescence

Epifluorescence cubes

Excitation lasers

STED Laser

Donut formation

Scanner

Objectives

Rainbow Spectral Detection Kit

Pinholes

Detectors

FLIM

RAYSHAPE Adaptive Optics system

FLEXPOSURE Adaptive Illumination

Software

Epifluorescence

Epifluorescence cubes

Excitation lasers

STED Laser

Donut formation

Scanner

Objectives

Emission filters

Pinholes

Detectors

FLIM

Software

Illumination

Cameras

Objectives

Filters

Resolution

Light sheets

Acquisition rate

Sample carrier frames

Environmental control

Software

Epifluorecence

Laser excitation wavelengths

Objectives

Filter cubes

Filter turret

Tube lenses

Camera

Software

Epifluorecence

Laser excitation wavelengths

Objectives

Cameras

Filter turret 1

Filter turret 2

Tube lenses

Relay lenses in front of ORCA Camera

Relay lenses in front of EM CCD Camera

Astigmatism lens (for 3D STORM)

SIM diffraction grating blocks

Image splitter

Software

Epifluorecence

Pinhole size [μm]
(dual disk)

Laser excitation wavelengths [nm]
(all CW)

Filter turret
– filter cubes for epifluorescence lamp