Confocal microscopy

Last modified by Mikko Liljeström on 2025/09/08 16:34

Equipment

Zeiss LSM 880

Zeiss inverted confocal microscope with GaAsP detector, AiryScan (Fast) detector, PicoQuant FLIM detector and a full environmental chamber.

LSM 880

Technical Information and capabilities

Objectives

Magnification

Objective type

NA

Working distance (mm)

phase contrast

Immersion

10x

Plan-Apochromat

0.45

2

-

Dry

20x

Plan-Apochromat

0.80

0.55

-

Dry

40x

C-Apochromat

1.20

0.28

-

Water

40x

Plan-Apochromat

1.40

0.13

-

Oil

63x

Plan-Apochromat

1.40

0.19

-

Oil

Laser lines

Laser

Wavelength (nm)

Example of fluorochromes

Diode

405

DAPI, Hoechst

Argon

458

CFP

Argon

488

FITC, Alexa Fluor 488, GFP, Cy2, SytoxGreen, Acr.Orange/DNA

Argon

514

YFP, Cy3

Diode

561

PI, TRITC/Rhodamine, Mitotracker Orange, Alexa Fluor 546, DsRed2, Alexa Fluor 594, Texas Red, HcRed1

Helium-Neon

633

Alexa 633, Cy5, APC, Alexa 660, Alexa 647

AiryScan Filters

  • Plate
  • BP 420-480 + BP 495-550
  • BP 420-480 + BP 495-620
  • BP 420-480 + LP 605
  • BP 465-505 + LP 525
  • BP 495-550 +LP 570
  • BP 570-620 + LP 645

Main Beam Splitters

  • MBS 458
  • MBS 458/514
  • MBS 458/461
  • MBS 488
  • MBS 488/561
  • MBS 488/561/633
  • MBS T89/R20
  • Plate

Secondary Beam Splitters

  • Mirror
  • SBS LP 490
  • SBS LP 515
  • SBS LP 545
  • SBS LP 635
  • SBS SP 545
  • SBS SP 610
  • Plate

Fluorescence filters for VIS-mode

Zeiss filter set 49

Zeiss filter set 38

Zeiss filter set 43

Zeiss filter set 50

DAPI/ Hoechst

FITC/ Alexa Fluor 488/ GFP

TRITC/ Cy3/ Alexa Fluor 546

Cy5, Alexa Fluor 647

Transmitted light in Bright-field and DIC (ask for the DIC prisms if you need them).

Detectors

  • 2 PMT detectors (One with extra cooling for increased sensitivity in infrared)
  • 1 GaAsP detector
  • Airyscan detector
  • Transmitted light detector (T-PMT)

Software and accessories for live cell and multi-well imaging

  • Zeis ZEN 2
  • Modules: Experiment designer, Tiles & Positions, FRAP and FRET
  • Definite Focus hardware autofocus system
  • Scanning stage for multipoint or mosaic imaging
  • Large environmental chamber
  • Incubator insert PM S1 (Temperature and CO2 control): Observation area 32 x 30 mm (oval) https://www.pecon.biz/products/product/?pid=5271%7CHeating_Insert_P_S
  • 40x and 63x water immersion objectives are available upon request
Environmental Chamber Temperature Setting

The readout of the temperature probe differs slightly from the media temperature in the sample chamber. To heat the sample to +37 C, adjust the Incubator to:

  • H Insert P +38.0 °C
  • H Unit XL +38.2 °C

Test your own fluorophores on this optical system

To do so, click on the link below, choose the right configuration and add your own fluorophore. You will see the efficiency of the system for that specific label.

https://www.fpbase.org/microscope/fGbZLzo4KpjDLnCZqK9m6G/

Keywords

Inverted microscope

Multi-well

Confocal/ multiphoton

Super-resolution

Incubator

Large environmental chamber

Definite focus

Water immersion

Leica SP8 CARS

Leica inverted multi-photon microscope with two HyD detectors, resonant scanner, tunable CARS laser and a full environmental chamber.

SP8 CARS

Technical Information and capabilities

Objectives

Magnification

Objective type

NA

Working distance (µm)

Immersion

Coverglass thickness (mm)

XY res. (nm)

Z res. (nm)

10x

HC PL APO CS

0.40

360

Multi

-

488

4093

25x

HCX IR APO L

0.95

2400

Water

0.17

205

550

20x

HC PL APO CS2

0.75

680

Multi

-

260

1108

40x

HC PL APO CS2

1.10

650

Water

0.14-0.18

177

377

63x

HC PL APO CS2

1.20

300

Water

0.14-0.18

163

290

63x

HC PL APO CS2

1.30

300

Glycerol

0.14-0.19

150

276

Single-photon laser lines

Laser

Wavelength (nm)

Example of fluorochromes

Diode (Violet)

405

DAPI, Hoechst

Argon (Blue)

458

CFP

Argon (Blue)

476

-

Argon (Blue)

488

FITC, Alexa Fluor 488, GFP, Cy2, SytoxGreen, Acr.Orange/DNA

Argon (Blue)

496

-

Argon (Blue)

514

YFP, Cy3

DPSS (Lime)

561

PI, TRITC/Rhodamine, Mitotracker Orange, Alexa Fluor 546, DsRed2, Alexa Fluor 594, Texas Red, HcRed1

Helium-Neon (Orange)

594

-

Helium-Neon (Red)

633

Alexa 633, Cy5, APC, Alexa 660, Alexa 647

Multiphoton laser (CARS, TPEF, SHG)

  • APE picoEmerald
  • Wavelengths: 1064.5 nm and tunable 780-940 nm

Detectors

  • 2 high sensitivity hybrid detectors (HyD)
  • 1 PMT detector
  • 2 reflected light non-descanned PMT detectors with the possibility for filters
  • 2 transmitted light non-descanned PMT detectors with the possibility for filters

Software and accessories for live cell and multi-well imaging

  • Full-enclosure type temperature-controlled environmental chamber for live-cell imaging and bleaching FRAP applications.
  • An inverted temperature-controlled slow-flow imaging chamber available on request

Keywords

Inverted microscope

Multi-well

CARS

Confocal/multi-photon

Live cell imaging

Environmental chamber

Water immersion

Leica TCS SP8 X

Leica TCS SP8 X with white light laser. Laser scanning confocal microscope for both fixed and live-cell imaging. Mounted on a motorized Leica inverted microscope.

SP8 X

Technical Information and capabilities

Objectives

Magnification

Objective type

NA

Working distance (µm)

Immersion

Coverglass thickness (mm)

XY res. (nm)

Z res. (nm)

10x

HC PL APO CS2

0.40

2740

Dry

0.17

488

2630

20x

HC PL APO CS2

0.75

620

Dry

0.17

260

649

40x

HC PL APO CS2

1.30

240

Oil

0.17

150

299

63x

HC PL APO CS2

1.40

140

Oil

0.17

139

236

63x

HC PL APO CS2

1.20

300

Water

0.14-0.18

163

290

Lasers

  • 405 nm diode
  • Supercontinuum laser, freely tunable between 470-670 nm, maximum of 8 simultaneous laser lines

Detectors, Software and accessories for live cell and multi-well imaging

  • 2 high sensitivity hybrid detectors (HyD)
  • 2 PMT detectors
  • 1 transmitted light detector (T-PMT)

The SP8 X has a full-enclosure type temperature-controlled environmental chamber for imaging live cells. While the chamber and microscope are heating up or cooling down the light path distances are constantly changing. Because of this it is not recommended to image while the chamber temperature is changing. To keep the chamber at a steady temperature, it should be either heated (+37 °C) or at room temperature for the whole day. The first reservation created for a given day determines the temperature of the system.

Keywords

 Inverted microscope

Multi-well

Confocal

Live cell imaging

Environmental chamber

White light laser

Leica Stellaris 8 FALCON / DLS

Stellaris FALCON

Leica Stellaris 8 inverted confocal microscope with 5 sensitive HyD detectors and tunable white-light laser excitation source.

Highlights:

  • FALCON module for fast fluorescence lifetime measurement
  • Digital Light-Sheet module
  • TauSense detection
  • Fast resonant scanner
  • LASX Navigator
  • Leica Lightning
  • NIR excitation (up to 790nm) and detection (up to 850nm)

The LMU have made a nice video covering the capabilities of the Stellaris 8 and its FALCON module (not DLS). Definitely worth a look.

Technical information:

Microscope

  • Leica DMi8 inverted microscope
  • Motorized scanning stage
  • AFC hardware autofocus
  • OKOlab full-enclosure incubator with temperature, CO2, and humidity control

Objectives

Magnification

Objective type

NA

Working distance (µm)

Immersion

Coverglass thickness (mm)

10x

HC PL APO CS2

0.40

2740

Dry

0.17

20x

HC PL APO CS2

0.75

620

Dry

0.17

40x

HC PL APO CS2 CORR

1.25

350

Glycerol

0.14-0.18

63x

HC PL APO CS2

1.40

140

Oil

0.17

63x

HC PL APO CS2 motCORR

1.20

300

Water

0.14-0.18

Lasers

  • 405 nm diode laser
  • 488 nm laser for FRAP
  • Supercontinuum laser, freely tunable between 440-790nm, maximum of 8 simultaneous laser lines

Scanner

Tandem scanner with both traditional point scanner and fast 8kHz resonant scanner.

Five sensitive HyD detectors:

  • 2 HyD S - all round detector for high performance detection throughout the spectrum
  • 2 HyD X - specialized for fast fluorescence lifetime imaging in the visible to the far-red
  • 1 HyD R - specialized for detection above 740nm (incl. fast fluorescence lifetime)

Please note that all 5 detectors are suitable for regular confocal imaging. However, the HyD X's and HyD R are not tolerant of over exposure. If overexposed they will shut down and may be permanently damaged. You can find out more about the Leica HyD detectors and their capabilities here.

Software Leica LAS X

  • 4.5.0
  • 4.6.0 (5.10.2023)
  • 4.7
  • 4.8 (31.12.2024)

Andor Dragonfly

Andor Dragonfly

Technical Information and capabilities

Andor Dragonfly 505

Objectives

Magnification

Objective type

NA

Working distance (mm)

Phase-contrast

Immersion

PFS

10x

Plan Fluor DL

0.30

15.2

Ph1

Dry

+

20x

Plan Apo  λ

0.75

1.0

-

Dry

+

40x 1), 2)

Apo LWD

1.15

0.6

-

Water

+

60x

Plan Apo VC

1.2

0.29

-

Water

+

100x 1)

SR Apo TIRF

1.49

0.12

-

Oil

+

40x

Plan Apo  λ

1.25

0.3

-

Silicone oil

+

1) Not Plan corrected

2) Suitable for NIR labels. Chromatic correction 405-950nm

Lasers

  • 404nm, 100mW
  • 488nm, 150mW
  • 561nm, 100mW
  • 642nm, 110mW
  • 730nm, 30mW

Filters

For visual inspection of your sample through the eyepiece
  • DAPI-50606
  • GFP-30309
  • TRITC-B 05
  • mCherry-C
For imaging
  • 445 -46 nm
  • 521 -38 nm
  • 594 -43 nm
  • 685 -47nm
  • 809 -90nm
  • TR-POL-DIC-FWL, Polarizer
  • 445/521/594/685/809

Cameras

  • Andor Zyla 4.2 sCMOS
  • Andor iXon 888 U3 EMCCD

Software

Test your own fluorophores on this optical system

To do so, click on the link below, choose the right configuration and add your own fluorophore. You will see the efficiency of the system for that specific label.

https://www.fpbase.org/microscope/MHoNXQQFSXUuAowQ34PYg8/?d=andor-ixon-life-888-bv

Data Transfers From the Dragonfly Computer

If you're exporting or transferring data from the Dragonfly computer and not using the microscope, please start the Fusion OFFLINE version from the desktop. Using the regular Fusion while the microscope is off will confuse it and cause problems to the next user.