Agora Instruments

Acquisition systems

Confocal

Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser confocal scanning microscopy (LCSM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a spatial pinhole to block out-of-focus light in image formation.^[1] Capturing multiple two-dimensional images at different depths in a sample enables the reconstruction of three-dimensional structures (a process known as optical sectioning) within an object.

Olympus FluoView 3000

Illumination	LED; pE-300white; CoolLED
Camera	Olympus DP80 Sensor:CCD color Number of pixels:4080 x 3072 Chip area: 8.8 x 6.6 mm Pixel chip size: 6.45 x 6.45 µm Dynamic range: 42 bit (colour)
Lasers	405nm 488nm 561nm 640nm
Objectives	Plan Apochromat 1.25x/0.04 WD 5.0mm no contrast dry Plan Apochromat 10x/0.4 WD 3.1mm DIC dry Plan Apochromat 20x/0.75 WD 0.6mm DIC dry Plan Fluorite 40x/1.3 WD 0.2mm DIC oil Plan Apochromat 60x/1.42 WD 0.15mm DIC oil
Stage	Motorized
Contrast	DIC
CO2 \| T° control	No
Detector type	1x T-PMT 4x GaAsP
Optional modules
Software	CellSens FluoView 31S-SW
Room	B25A.03.201

Super Resolution Microscopy

Super resolution microscopy goes beyond the limitations of conventional microscopy by allowing researchers to visualize intricate details at the sub-organelle level. The microscope can incorporate advanced techniques such as Lattice SIM², SIM² Apotome, widefield DIC, SMLM, and TIRF, enabling the correlation of images from the same sample to reveal molecular details with exceptional clarity and precision. This cutting-edge technology provides insights into cellular structures and processes at scales previously unattainable, making it a powerful tool for biological research across various applications.

Zeiss Elyra 7

Model	Zeiss Axio Observer 7 SR RP stand for Elyra 7, Inverted
Widefield Illumination	HXP 120 V
Lasers	405 nm (50 mW) 488 nm (500mW) 561 nm (500 mW) 642 nm (500 mW)
Filters	DAPI (BP 420-480) GFP (BP 495-550) Rhodamin (BP 570-620) Cy5 (LP 655)
Objectives	Plan Neofluar 10x / NA 0.30 / dry /WD 5.2mm Plan Apochromat 20x / NA 0.8 / dry / WD 0.55mm Plan Apochromat 40x / NA 1.4 / oil / WD 0.13mm Plan Apochromat 63x / NA 1.4 / oil / WD 0.19mm α Plan Apochromat 63x TIRF / NA 1.46 / oil / WD 0.10mm
Stage	Motorized Piezo (Z direction) Definite Focus 3
Contrast	No
CO2 \| T° control	Yes both
Incubation	Full enclosure / Dark
Cameras	2x PCO Edge sCMOS DuoLink (simultaneous two-color Imaging)
Imaging Modalities	Widefield Lattice SIM2 Single-Molecule Localization Microscopy Apotome HILO/TIRF
Software	Zeiss Zen Black 3.0 SR
Room	B25A.03.201

Spinning Disk | Time-Lapse

Spinning-disk (Nipkow disk) confocal microscopes use a series of moving pinholes on a disc to scan spots of light. Since a series of pinholes scans an area in parallel, each pinhole is allowed to hover over a specific area for a longer amount of time thereby reducing the excitation energy needed to illuminate a sample when compared to laser scanning microscopes. Decreased excitation energy reduces phototoxicity and photobleaching of a sample often making it the preferred system for imaging live cells or organisms.

Nikon Ti2 | Yokogawa CSU-W1

Widefield LED Illumination	Lumencore Spectra X LED 395nm 440nm 470nm 508nm 555nm 640nm
Filter Cubes	Quintuple multiband filtercube for DAPI/FITC/TRITC/Cy5/Cy7 (32mm) DAPI-5060C Filter Cube (32mm) GFP-4050B Filter Cube (32mm) Cy3-4040C Filter Cube (32mm) Cy5-4040C Filter Cube (32mm)
Spinning Disk laser excitation	Omicron modified LightHUB+ 405nm 488nm 561nm 638nm
Objectives	CFI Plan Apochromat Lambda 10X, N.A. 0.45, W.D. 4.0mm CFI Plan Apochromat Lambda 20X, N.A. 0.75, W.D. 1.0mm, spring-loaded CFI Plan Fluorite 40X, N.A. 0.75, W.D. 0.66mm CFI Plan Apochromat Lambda 60x, N.A. 0.95, W.D. 0.21mm, Spring-loaded CFI Plan Apochromat Lambda 60X Oil, N.A. 1.40, W.D. 0.13mm CFI Plan Fluorite 100X Oil, N.A. 1.30, W.D. 0.16mm
Stage	Motorized Piezo (Z direction) Nikon PFS (Perfect Focus System)
Contrast	DIC
CO2 \| T° control	Yes [Full enclosure]
Cameras	2x Photometrics Prime 95B 1x Nikon DS-Qi2
Optional modules	JOBS General Analysis 3 Deconvolution
Software	Nikon NIS-Elements AR 5.0
Room	B25A.03.201

Widefield | Fluorescence

The majority of fluorescence microscopes, especially those used in the life sciences, are of the epifluorescence design shown in the diagram. Light of the excitation wavelength illuminates the specimen through the objective lens. The fluorescence emitted by the specimen is focused to the detector by the same objective that is used for the excitation which for greater resolution will need objective lens with higher numerical aperture. Since most of the excitation light is transmitted through the specimen, only reflected excitatory light reaches the objective together with the emitted light and the epifluorescence method therefore gives a high signal-to-noise ratio. The dichroic beamsplitter acts as a wavelength specific filter, transmitting fluoresced light through to the eyepiece or detector, but reflecting any remaining excitation light back towards the source.

Zeiss | Widefield

Stage	Zeiss Axio Observer Z1, Inverted
Illumination	X-Cite
Filter Cubes	DAPI GFP Rhodamin Cy5
Objectives	Plan Apochromat 10X, N.A. 0.45, air, DIC, W.D. 2.0mm Plan Apochromat 20X, N.A. 0.8, air, DIC, W.D. 0.55mm EC Plan Neofluar 40X, N.A. 1.3, Oil, DIC, W.D. 0.21mm Plan Apochromat 63X, N.A. 1.4, Oil, DIC, W.D. 0.19mm
Stage	Motorized
Contrast	DIC
CO2 \| T° control	No \| No
Cameras	Axiocam 506 color Axiocam 506 mono
Optional modules	Tile (Image stitching)
Software	Zeiss Zen 2.6 Blue edition
Room	B25A.03.201

Slide scanner

A slide scanner allows you to digitize full microscopy slides in an automated manner. This is a high througput system able to process around a hundred of slides in one batch.

Zeiss Axioscan 7

Illumination	Zeiss Colibri 7 Type R[G/Y]CBV-UV Far Red (735nm) for excitation of Alexa Fluor 750, Cy7 and similar dyes Red (631nm) for excitation of Cy5, Alexa 631, TOTO-3 and similar dyes Yellow (590nm) for excitation of mCherry, Alexa 568, mPlum and similar dyes Green (555nm) for excitation of Cy3, TRITC, DsRed and similar dyes (Cyan (511nm) for excitation of eYFP, Eosin, TOTO-1 and similar dyes) no filters available Blue (469nm) for excitation of eGFP, Fluo4, FITC and similar dyes (Violet (423nm) for excitation of eCFP, Lucifer Yellow, Alexa 430 and similar dyes) no filters available UV (385nm) for excitation of DAPI, Alexa 405, Hoechst 33258 and similar dyes
Filters	BFP: EX 390/40, DM 420, EM 450/40, 96 HE BFP shift free eGFP: 470/40, 495, 525/50, 38 HE eGFP shift free Cy3: 550/25, 570, 605/70, 43 HE Cy3 shift free mPlum: 587/25, 605, 647/70, 64 HE mPlum shift free Cy5: 640/30, 660, 690/50, 50 Cy5 shift free Cy7: 734/40, 762, 785/38, 110 HE LED
Objectives	Fluar 5x/0.25 Plan Apochromat 10x/0.45 Plan Apochromat 20x/0.80 Plan Apochromat 40x/0.95
Stage	Motorized
Contrast	Brightfield, Transfer of Intensity Equation (TIE), Fluorescence
CO2 \| T° control	No
Cameras	Color camera Zeiss Axiocam 705 for Axio Scan 7 Black and White Camera Orca Flash 4.0 V3 for Axio Scan 7
Optional modules	NC
Software	Zen Blue 3.5
Room	B25A.03.201

Image Processing

[Under construction]