Confocal, Super-Resolution and Digital Light-Sheet Microscopes

The Leica SP8 spectral confocal microscope is equipped with three high sensitivity, low-noise hybrid detectors capable of photon counting and two conventional PMT detectors. Sample excitation can be accomplished by multiple lasers including a pulsed white light laser tunable from 470 to 670 nm that allows selection of the optimal excitation wavelength; the LightGate panchromatic electronic barrier filter allows gating of the detectors to avoid collecting signal during the laser pulse so that only pure emission signals are collected. The system also has conventional fixed laser excitation lines at 405, 458, 476, 488, 496 and 514 nm. For two-photon imaging, including FLIM-FRET, the system has a MaiTai DeepSee Ti-Sapphire ultrafast laser (tunable between 680–1060 nm). The SP8 is equipped with both a conventional point scanner for work requiring the highest sensitivity and a resonant scanner for live cell imaging (28 fps at 512x512). An environmental chamber for temperature and CO2 control during prolonged live-cell imaging experiments is available. Complex experimental designs, 3D image tiling and 3D rendering and measurements are possible with the LAS AF Leica software.
The Leica confocal microscope has been upgraded with a 3D STED super-resolution system. This system can achieve a resolution of 50 nm or less. Three depletion lasers (592, 660 and 775 nm) enable multicolor detection of a wide range of fluorophores. Use of the Huygens deconvolution software programs allows for further improved resolution.
Download an STED technology basics and sample preparation guide (PDF).
The following objectives are available for this system:
Mag. | Objective Description | NA | Immersion Medium | Working distance (mm) |
---|---|---|---|---|
10x | HC PL APO CS | 0.40 | Air | 2.20 |
20x | HC PL APO CS | 0.70 | Air | 0.59 |
20x | HC PL APO IMM CORR CS2 | 0.75 | Water, glycerol, or oil | 0.68 |
25x | HCX IRAPO L | 0.95 | Water | 2.40 |
40x | HC PL APO CS2 | 1.10 | Water | 0.65 |
40x | HC PL APO CS2 | 1.30 | Oil | 0.24 |
63x | HC PL APO CS2 | 1.40 | Oil | 0.14 |
63x | HC PL APO CORR CS2 | 1.30 | Glycerol | 0.30 |
63x | HC PL APO CORR CS2 | 1.20 | Water | 0.30 |
100x | HCX PL APO CORR CS | 1.44 | Oil | 0.10 |
100x | HC PL APO STED WHITE | 1.40 | Oil | 0.13 |
Download the free Leica LAS X Core Offline software. Scroll down to Downloads.
The Leica GSD 3D super-resolution microscope with TIRF possesses four different laser lines (488, 560, 642 and 405 nm) and a fast, highly sensitive Andor iXon Ultra 897 EMCCD camera for detecting up to three fluorophores. The microscope also includes a fully automated TIRF system allowing super-resolution to be combined with TIRF microscopy.
Download the GSD miscroscopy basics and sample preparation protocol (PDF).
The following objectives are available for use with the GSD system:
Mag. | Objective Description | NA | Immersion Medium | Working distance (mm) |
---|---|---|---|---|
10x | HCX PL FLUOTAR | 0.30 | Air | 11 |
100x | HC PL APO CORR TIRF | 1.47 | Oil | 0.09 |
160x | HC PL APO | 1.43 | Oil | 0.07 |
The Leica TCS SP8 system possesses fixed diode laser lines (405, 488, 552, 638 nm) that can be utilized for conventional confocal microscopy or digital light-sheet applications. Illumination with the light sheet allows rapid acquisition of multiple images (>100 frames/second) to permit 3D rendering and results in low phototoxicity. Imaging can be performed for entire organs (e.g., Arabidopsis roots) or organisms (e.g., Drosophila embryos, developing zebra fish). Extended time-lapse acquisition can be used to monitor physiological or developmental changes over time.
Download the Leica SP8 Digital Light Description (PDF).
The following objectives are available for use with the confocal and light-sheet systems:
Mag. | Objective Description | NA | Immersion Medium | Working distance (mm) |
---|---|---|---|---|
10x | HC PL APO CS | 0.40 | Air | 2.20 |
20x | HC PL APO CS | 0.70 | Air | 0.59 |
20x | HC PL APO IMM CORR CS2 | 0.75 | Water, glycerol, or oil | 0.68 |
25x | HCX IRAPO L | 0.95 | Water | 2.40 |
40x | HC PL APO CS2 | 1.10 | Water | 0.65 |
40x | HC PL APO CS2 | 1.30 | Oil | 0.24 |
63x | HC PL APO CS2 | 1.40 | Oil | 0.14 |
63x | HC PL APO CORR CS2 | 1.30 | Glycerol | 0.30 |
63x | HC PL APO CORR CS2 | 1.20 | Water | 0.30 |
100x | HCX PL APO CORR CS | 1.44 | Oil | 0.10 |
100x | HC PL APO STED WHITE | 1.40 | Oil | 0.13 |
The following objectives are specifically for use with the light-sheet system:
Mag. | Objective Description | NA | Immersion Medium | Working distance (mm) |
---|---|---|---|---|
2.5x | HC PL FLUOTAR | 0.07 | Air | 9.4 |
10x | HC APO DLS L | 0.30 | Water | 3.6 |
25x | HC PL APO IMM CORR CS2 | 0.75 | Water | 2.5 |
Widefield Microscopes
The Zeiss Axiovert 200M inverted microscope is a fully automated instrument with a motorized stage and z-drive. This microscope is capable of brightfield and DIC. A featured technique on this system is slide scanning (the automated acquisition of images across a defined region), with the possibility of acquiring high-quality composite images from whole-tissue slides. A wide range of low and high magnification objectives are available. The selection of cameras includes a Leica DFC290 color camera. An environmental chamber with temperature and CO2 control is available for extended imaging of live cells. The system operates under control of the MetaMorph software v.7.8.12.
The following objectives are available for this system:
Mag. | Objective Description | NA | Immersion Medium | Working distance (mm) | Application |
---|---|---|---|---|---|
5x | Plan Apochromat | 0.16 | Air | 12.1 | BF |
10x | EC Plan-NeoFluar | 0.3 | Air | 5.6 | BF, DIC II |
20x | Plan-Apochromat | 0.75 | Air | 0.61 | BF, DIC II |
20x | Plan-Apochromat | 0.8 | Air | 0.55 | BF, DIC II |
25x | LCI Plan-NeoFluar | 0.8 | Water/glycerol | 0.21 | BF |
40x | LD Plan-NeoFluar | 0.6 | Air | 2.5-3.3 | BF |
40x | EC Plan-NeoFluar | 1.3 | Oil | 0.21 | BF, DIC III |
40x | C-Apochromat | 1.2 | Water | 0.29 | BF, DIC III |
40x | C-Apochromat | 1.2 | Water | 0.28 | BF, DIC III |
63x | Plan-Apochromat | 1.4 | Oil | 0.18 | BF, DIC III |
63x | Plan-Apochromat DIC | 1.4 | Oil | 0.18 | BF, DIC III |
63x | C-Apochromat | 1.2 | Water | 0.28 | BF |
BF-bright field, DIC-differential interference contrast

The Zeiss Axiovert 200M inverted microscope is a fully automated instrument with a motorized stage and z-drive. A featured technique on this system is fluorescent microscopy; however, the system is also capable of transmitted light bright-field. In addition, the microscope can acquire high-quality composite images of whole-tissue slices (a process termed "tiling") for both single- and multi-channel fluorescence. A wide range of objectives and fluorescence filter sets are available. Images are acquired by a Hamamatsu ORCA-ER CCD camera, a high sensitivity, low-noise device for high resolution imaging. An environmental chamber with temperature and CO2 control is available for extended imaging of live cells. The system operates under the control of the MetaMorph v.7.8.12 software program. This program enables complex experimental designs, including time-lapse imaging, autofocusing, streaming and z-stack acquisition.
The following objectives are available for this system:
Mag. | Objective Description | NA | Immersion Medium | Working distance (mm) | Pixel size (um) | Field of view |
---|---|---|---|---|---|---|
5x | Plan Apochromat | 0.16 | Air | 12.1 | ||
10x | EC Plan-NeoFluar | 0.3 | Air | 5.6 | 0.9958 | 1338.4 x 1019.7 |
20x | Plan-Apochromat | 0.75 | Air | 0.61 | ||
20x | Plan-Apochromat | 0.8 | Air | 0.55 | 0.4959 | 666.4 x 507.8 |
25x | LCI Plan-NeoFluar | 0.8 | Water/glycerol | 0.21 | 0.3947 | 530.5 x 404.2 |
40x | LD Plan-NeoFluar | 0.6 | Air | 2.5-3.3 | 0.2490 | 334.7 x 255.0 |
40x | EC Plan-NeoFluar | 1.3 | Oil | 0.21 | 0.2490 | 334.7 x 255.0 |
40x | C-Apochromat | 1.2 | Water | 0.29 | ||
40x | C-Apochromat | 1.2 | Water | 0.28 | 0.2454 | 330.0 x 251.3 |
63x | Plan-Apochromat | 1.4 | Oil | 0.18 | 0.1569 | 210.9 x 160.7 |
63x | Plan-Apochromat DIC | 1.4 | Oil | 0.18 | 0.1569 | 210.9 x 160.7 |
63x | C-Apochromat | 1.2 | Water | 0.28 | 0.1576 | 211.8 x 161.4 |
The following fluorescent filters are available for this microscope:
Fluor | Filter Set | Excitation | Emission |
---|---|---|---|
DAPI | 49000 | 325-375 | 435-485 |
DAPI LP | FS2 | 365 | LP420 |
CFP | FS 47 | 426-446 | 460-500 |
eGFP/FITC | 49002 | 450-490 | 500-550 |
YFP | FS 46 | 490-510 | 520-550 |
Cy3/TRITC | 49004 | 532-557 | 570-640 |
DSRed | 49005 | 530-560 | 590-650 |
Cy5 | 49006 | 590-650 | 662-737 |
Cy7 | 49007 | 642-747 | 765-855 |

The Leica DM5500 upright microscope is an automated instrument with a motorized z-drive and fluorescence filter wheel, and automatic selection of appropriate optical components for every featured microscopy modality. The microscope is capable of transmitted light brightfield, dark field, phase contrast, DIC and fluorescence imaging. Images can be captured with a Leica DFC290 high resolution color camera or a Leica DFC340 high sensitivity cooled monochrome camera. The system features a fully integrated deconvolution module with 3D Blind, 3D Non-Blind, Golds and inverse filter deconvolution algorithms.
The following objectives are available for this system:
Mag. | Objective Description | NA | Immersion Medium | Working distance (mm) |
---|---|---|---|---|
5x | N PLAN PH 0 | 0.12 | Air | 14.0 |
10x | HC PL FLUOTAR | 0.30 | Air | 11.0 |
20x | HCX PL FLUOTAR | 0.50 | Air | 1.15 |
40x | HCX PL FLUOTAR | 0.75 | Air | 0.40 |
40x | HC PL APO CS2 | 0.13 | Oil | 0.24 |
63x | HCX PL APO | 1.40 | Oil | 0.10 |
63x | HC PL APO CS2 CORR | 1.20 | Water | 0.30 |
100x | HCX PL APO CS CORR | 1.44 | Oil | 0.10 |
The following fluorescent filter cubes are available for the Leica DM 5500B microscope:
Filter Cube | Excitation range | Dichromatic mirror | Suppression filter |
---|---|---|---|
A4 | UV | 400 | BP 470/40 |
L5 | Green | 505 | BP 527/30 |
N3 | Blue | 565 | BP 640/40 |

The Thunder Imager Model Organism stereomicroscopy system enables fast and easy 3D exploration of whole model organisms and complex tissue cultures marked with fluorescent reporters. The system utilizes Computational Clearing to remove out-of-focus blur and deliver clear images in real time. At the core of the system is a Leica M205 FA automated stereo microscope with a motorized XY stage that is ideally suited for scanning large areas at high magnification. Acquisition of composite images is facilitated by the Navigator software. The XY scanning stage is also useful for time-lapse experiments or high throughput screening of samples in multiwell plates. The microscope is equipped with 0.63x, 1x and 2x objective lenses enabling magnification up to 320x. Images can be acquired with a highly sensitive high-speed Leica DFC9000 GT 4.2-megapixel sCMOS monochrome camera (pixel size 6.5 x 6.5 µm) or a high-resolution Leica DMC5400 20.5-megapixel CMOS color camera (pixel size 2.4 x 2.4 µm).
Sample illumination options include a LED3 fluorescence light source with white light output of 390-680 nm, an objective-mountable O-ring illuminator with 48 LEDs, a KL2500 LED illuminator with flexible gooseneck light guides and a TL5000 Ergo transmitted light base. Various accessories for glare-free imaging in incident light are available. Samples can be also viewed and imaged in polarized light. A heated glass plate creates a warm transparent surface for working with embryos, organoids, and other living specimens.
The following objectives are available for this stereo microscope:
Magnification | Objective description | NA | Working distance (mm) |
0.63x | Plan Apo | 67 | |
1x | Plan Apo | 0.35 | 61.5 |
2x | Plan Apo with correction collar for samples immersed in water | 0.35 | 20.1 |
The following fluorescent filter sets are available for this stereo microscope:
Filter set | Filter set number | Excitation (nm) | Dichroic | Emission (nm) |
DAPI BP | 49028 | 383-407 | 425 LP | 435-485 |
eCFP | 49001 | 426-446 | 455 LP | 460-500 |
eGFP | 49002 | 450-490 | 455 LP | 500-550 |
eYFP | 49003 | 480-520 | 455 LP | 520-550 |
dsRed | 49005 | 530-560 | 455 LP | 590-65 |
mCherry/Texas Red | 49008 | 540-580 | 455 LP | 593-667 |
Cy5 | 49006 | 590-650 | 455 LP | 663-737 |
Options for sample imaging


The Leica M205 FA stereo microscope is a fully automated instrument with a motorized z-drive, focus, zoom and filter wheel controls for multichannel time-lapse experiments. The available filter sets include DAPI, CFP, GFP, YFP and dsRed. The featured objective has a zoom range of 20.5:1 and a working distance of 61.5 mm. The system includes a transmitted light base as well as an O-ring LED illuminator with 48 LEDs. Images are captured with a 2.8 Mpixel Leica DFC7000T color, high-sensitivity, cooled digital camera.
Some special features include Automontage software for extended depth of focus imaging and Rotterman's relief contrast to visualize unstained transparent objects. The system also features a PhotoFluor II illuminator which is an adjustable fluorescence light source providing a very stable high-power output essential for time-lapse and quantitative fluorescent imaging.
Montage image below taken by Michele Warmund. Right image is the multifocus image, and left image is one of the single images in the stack.


The following fluorescent filters are available for the Leica M205 FA stereo microscope:
More example montage images (Michele Warmund):


An inverted, fully automated Leica DMI4000 B with integrated Eppendorf Microinjection system and a 1.4 megapixel, 12-bit, cooled CCD camera from Q-Imaging. This system is capable of injecting a single cell with volumes as small as a femtoliter. The capture software from Q-Imaging allows for quick and easy collection of images for traditional microscopy applications as well.
This system is equipped with four objective lenses:
Mag. | Objective Description | NA | Immersion Medium | μm per pixel | Field of View (μm) | Working Distance(mm) | Applications* |
---|---|---|---|---|---|---|---|
5x | N Plan | 0.12 | Air | 1.85874 | 2587.36 x 1933.09 | 14 | BF, FL, Ph0, DIC |
10x | N Plan | 0.25 | Air | 0.945017 | 1315.46 x 982.82 | 5.8 | BF, FL, Ph1, DIC |
20x | N Plan Corr | 0.4 | Air | 0.464134 | 646.07 x 482.69 | 3.2-1.9 | BF, FL, Ph1, DIC |
40x | HCX PL Fluotar L Corr | 0.6 | Air | 0.229084 | 318.88 x 238.25 | 3.3-1.9 | BF, FL, Ph2, DIC |
The following filters are available on this system:
The following are example images taken by MU researchers:

Diatomes imaged using DIC (Differential Interference Contrast) for enhanced details

Diatomes imaged using Phase Contrast, a technique different than DIC, but also for enhancing certain details.

A cell being injected

Nuclear transfer in an oocyte. Taken by Ye Yuan
Image analysis/processing
- Huygens Professional: Rapid 2D and 3D deconvolution of confocal, STED and widefield images.
- Metamorph: image analysis, object counting, morphological analysis, thresholding, 3D reconstruction/rotation of confocal optical sections.
- Imaris: 3D reconstruction of optical sections, measurements in 3D, isosurfacing, animations, colocalization analysis.
- Adobe Photoshop: image processing and editing with batch mode.
- Leica LAS X 3D Analysis and Measurements: 3D multichannel analysis, measurements and object classification.
- Fiji/ImageJ: image processing and analysis.
Sample preparation
-
Leica CM3050 S Cryostat for cutting 0.5-300 micron-thick tissue sections of frozen samples.
-
Leica ARTOS 3D Ultramicrotome for cutting semi-thin and thin sections of resin-embedded samples for light and electron microscopy.
-
Paraffin Microtome for cutting 1-50 micron thick paraffin sections.
-
Vibratome 3000 Plus for cutting variable thicknesses as thin as 100 µm of live or fixed specimens with a maximum specimen size of 60x40x15mm.
Supply center
ALMC has an on-site Supply center stocked with fluorescent secondary antibodies and markers. Consumables for laser capture microdissection are also available. In addition to our normal inventory, clients may special order anything from the Life Technologies catalog without shipping fees.
File transfer system
ALMC has a server that can be remotely accessed from any computer on the MU campus. It serves as a TEMPORARY holding place for files to facilitate transfer of the data you generate at the core to a local computer in your lab/office. Please note that due to space limitations the storage space is cleared every morning at 8:00 am, such that your files will only be stored for a maximum of 24 hours and you need to transfer them to your computer on the same day they were placed on the server. For instructions on connecting to this utility contact ALMC staff.