Confocal microscopy

Confocal microscopy
MeSH D018613
OPS-301 code 3-301
File:Confocalprinciple in English.svg
Principle of confocal microscopy

Confocal microscopy is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of adding a spatial pinhole placed at the confocal plane of the lens to eliminate out-of-focus light.[1] It enables the reconstruction of three-dimensional structures from the obtained images. This technique has gained popularity in the scientific and industrial communities and typical applications are in life sciences, semiconductor inspection and materials science.

Basic concept

File:Minsky Confocal Reflection Microscope.png
Confocal point sensor principle from Minsky's patent

The principle of confocal imaging was patented in 1957 by Marvin Minsky[2][3] and aims to overcome some limitations of traditional wide-field fluorescence microscopes. In a conventional (i.e., wide-field) fluorescence microscope, the entire specimen is flooded evenly in light from a light source. All parts of the specimen in the optical path are excited at the same time and the resulting fluorescence is detected by the microscope's photodetector or camera including a large unfocused background part. In contrast, a confocal microscope uses point illumination (see Point Spread Function) and a pinhole in an optically conjugate plane in front of the detector to eliminate out-of-focus signal - the name "confocal" stems from this configuration. As only light produced by fluorescence very close to the focal plane can be detected, the image's optical resolution, particularly in the sample depth direction, is much better than that of wide-field microscopes. However, as much of the light from sample fluorescence is blocked at the pinhole, this increased resolution is at the cost of decreased signal intensity – so long exposures are often required.

As only one point in the sample is illuminated at a time, 2D or 3D imaging requires scanning over a regular raster (i.e., a rectangular pattern of parallel scanning lines) in the specimen. The achievable thickness of the focal plane is defined mostly by the wavelength of the used light divided by the numerical aperture of the objective lens, but also by the optical properties of the specimen. The thin optical sectioning possible makes these types of microscopes particularly good at 3D imaging and surface profiling of samples.

Techniques used for horizontal scanning

Four types of confocal microscopes are commercially available:

  • Confocal laser scanning microscopes use multiple mirrors (typically 2 or 3 scanning linearly along the x and the y axis) to scan the laser across the sample and "descan" the image across a fixed pinhole and detector.
  • 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 photo-toxicity and photo-bleaching of a sample often making it the preferred system for imaging live cells or organisms.
  • Microlens enhanced or dual spinning disk confocal microscopes work under the same principles as spinning-disk confocal microscopes except a second spinning disk containing micro-lenses is placed before the spinning disk containing the pinholes. Every pinhole has an associated micro-lens. The micro-lenses act to capture a broad band of light and focus it into each pinhole significantly increasing the amount of light directed into each pinhole and reducing the amount of light blocked by the spinning disk. Microlens enhanced confocal microscopes are therefore significantly more sensitive than standard spinning disk systems. Yokogawa Electric invented this technology in 1992.[4]
  • Programmable array microscopes (PAM) use an electronically controlled spatial light modulator (SLM) that produces a set of moving pinholes. The SLM is a device containing an array of pixels with some property (opacity, reflectivity or optical rotation) of the individual pixels that can be adjusted electronically. The SLM contains microelectromechanical mirrors or liquid crystal components. The image is usually acquired by a charge coupled device (CCD) camera.

Each of these classes of confocal microscope have particular advantages and disadvantages. Most systems are either optimized for recording speed (i.e. video capture) or high spatial resolution. Confocal laser scanning microscopes can have a programmable sampling density and very high resolutions while Nipkow and PAM use a fixed sampling density defined by the camera's resolution. Imaging frame rates are typically slower for single point laser scanning systems than spinning-disk or PAM systems. Commercial spinning-disk confocal microscopes achieve frame rates of over 50 per second[5] – a desirable feature for dynamic observations such as live cell imaging.

In practice, Nipkow and PAM allow multiple pinholes scanning the same area in parallel[6] as long as the pinholes are sufficiently far apart.

Cutting-edge development of confocal laser scanning microscopy now allows better than standard video rate (60 frames per second) imaging by using multiple microelectromechanical scanning mirrors.

Confocal X-ray fluorescence imaging is a newer technique that allows control over depth, in addition to horizontal and vertical aiming, for example, when analyzing buried layers in a painting.[7]

Variants and enhancements

Improving axial resolution

The point spread function of the pinhole is an ellipsoid, several times as long as it is wide. This limits the axial resolution of the microscope. One technique of overcoming this is 4π microscopy where incident and or emitted light are allowed to interfere from both above and below the sample to reduce the volume of the ellipsoid. An alternative technique is confocal theta microscopy. In this technique the cone of illuminating light and detected light are at an angle to each other (best results when they are perpendicular). The intersection of the two point spread functions gives a much smaller effective sample volume. From this evolved the single plane illumination microscope.

Super resolution

There are confocal variants that achieve resolution below the diffraction limit such as stimulated emission depletion microscopy (STED). Besides this technique a broad variety of other (not confocal based) super-resolution techniques is available like PALM, (d)STORM, SIM, and so on. They all have their own advantages like ease of use, resolution and the need for special equipment/buffers/fluorophores/... .

Low-temperature operability

To image samples at low temperature, two main approaches have been used, both based on the laser scanning confocal microscopy architecture. One approach is to use a continuous flow cryostat: only the sample is at low temperature and it is optically addressed through a transparent window.[8] Another possible approach is to have part of the optics (especially the microscope objective) in a cryogenic storage dewar.[9] This second approach, although more cumbersome, guarantees better mechanical stability and avoids the losses due to the window.



The beginnings: 1940 - 1957

Scheme from Minsky's patent application showing the principle of the transmission confocal scanning microscope he built.

In 1940 Hans Goldmann, ophthalmologist in Bern, Switzerland, developed a slit lamp system to document eye examinations.[10] This system is considered by some later authors as the first confocal optical system.[11][12]

In 1943 Zyun Koana published a confocal system.[13] The article is written in Japanese before the Tōyō kanji-reform and no translation is available,[11] so it is not clear what this system actually is. A figure in this publication, however, clearly shows a confocal transmission beam path. In 1951 Hiroto Naora, a colleague of Koana, described a confocal microscope in the journal Science for spectrophotometry.[14]

The first confocal scanning microscope was built by Marvin Minsky in 1955 and a patent was filed in 1957. The scanning of the illumination point in the focal plane was achieved by moving the stage. No scientific publication was submitted and no images made with it were preserved.[15][16]

The Tandem-Scanning-Microscope

Scheme of Petráň's Tandem-Scanning-Microscope. Red bar added to indicate the Nipkow-Disk.

In the 1960s, the Czechoslovak Mojmír Petráň from the Medical Faculty of the Charles University in Plzeň developed the Tandem-Scanning-Microscope, the first commercialized confocal microscope. It was sold by a small company in Czechoslovakia and in the USA by Tracor-Northern (later Noran). It uses a rotating Nipkow disk to generate multiple excitation and emission pinholes.[12][17]

The Czechoslovak patent was filed 1966 by Petráň and Milan Hadravský, a Czechoslovak coworker. A first scientific publication with data and images generated with this microscope was published in the journal Science in 1967. Authors were M. David Egger from Yale University and Petráň.[18] In the footnotes of this paper it is mentioned that Petráň designed the microscope and supervised its construction and that he was partially a „research associate“ at Yale. A second publication from 1968 described theory and technical details of the instrument and had Hadravský and Robert Galambos, the head of the group at Yale, as additional authors.[19] In 1970 the US patent was granted which was filed in 1967.[20]

1969: The first confocal laser scanning microscope

In 1969 and 1971, M. David Egger and Paul Davidovits from Yale University, published two papers describing the first confocal laser scanning microscope.[21][22] It was a point scanner, meaning just one illumination spot was generated. It used epi-Illumination-reflection microscopy for the observation of nerve tissue. A 5 mW Helium-Neon-Laser with 633 nm light was reflected by a semi-transparent mirror towards the objective. The objective was a simple lens with a focal length of 8.5 mm. As opposed to all earlier and most later systems, the sample was scanned by movement of this lens (objective scanning), leading to a movement of the focal point. Reflected light came back to the semitransparent mirror, the transmitted part was focused by another lens on the detection pinhole behind which a photomultiplier tube was placed. The signal was visualized by a CRT of an oscilloscope, the cathode ray was moved simultaneously with the objective. A special device allowed to make Polaroid photos, three of which were shown in the 1971 publication.

The authors speculate about fluorescent dyes for in vivo investigations. They cite Minsky‘s patent, thank Steve Baer, at the time a doctoral student at the Albert Einstein School of Medicine in New York City where he developed a confocal line scanning microscope,[23] for suggesting to use a laser with ‚Minsky‘s microscope‘ and thank Galambos, Hadravsky and Petráň for discussions leading to the development of their microscope. The motivation for their development was that in the Tandem-Scanning-Microscope only a fraction of 10−7 of the illumination light participates in generating the image in the eye piece. Thus, image quality was not sufficient for most biological investigations.[11][24]

1977 – 1985: point scanners with lasers and stage scanning

In 1977 Colin J. R. Sheppard and A. Choudhury, Oxford, UK, published a theoretical analysis of confocal and laser-scanning microscopes.[25] It is probably the first publication using the term „confocal microscope“.[11][24]

In 1978 the brothers Christoph Cremer and Thomas Cremer in Heidelberg published a design for a confocal laser-scanning-microscope for fluorescent excitation with electronic autofocus. They also suggested a laser point illumination by using a „4π-point-hologramme“.[24][26]

In 1978 and 1980, the Oxford-group around Sheppard and Tony Wilson described a confocal with epi-laser-illumination, stage scanning and photomultiplier tubes as detectors. The stage could move along the optical axis, allowing optical serial sections.[24]

Fred Brakenhoff and coworkers showed in 1979 that the theoretical advantages of optical sectioning and resolution improvement are indeed achievable. In 1985 the group was the first to publish convincing images with regard to cell biological questions, followed shortly afterwards by other groups.[27]

In 1983 I. J. Cox und Sheppard from the Oxford group published the first work connecting a confocal with a computer. The first commercial laser scanning microscope, the stage-scanner SOM-25 was offered by Oxford Optoelectronics (after several take-overs acquired by BioRad) starting in 1982. It was based on the design of the Oxford group.[12][28]

Starting 1985: Laser point scanners with beam scanning

In the Mid-1980's, W. B. Amos, J. G. White and colleagues in Cambridge built the first confocal beam scanning microscope. The stage with the sample was not moving, instead the illumination spot was, allowing faster image acquisition: four images per second with 512 lines each. Hugely magnified intermediate images, due to a 1-2 meter long beam path, allowed the use of a conventional iris diaphragm as a ‘pinhole’, with diameters ~ 1 mm. First micrographs were taken with long-term exposure on film before a digital camera was added. A further improvement allowed zooming into the preparation for the first time. Zeiss, Leitz and Cambridge Instruments had no interest in a commercial production. The Medical Research Council (MRC) finally sponsored development of a prototype. The design was acquired by Bio-Rad, amended with computer control and commercialized as ‘MRC 500’. The successor MRC 600 was later the basis for the development of the first two-photon-fluorescent microscope developed 1990 at Cornell University.[27]

Developments at the University of Stockholm around the same time led to a commercial clsm distributed by the Swedish company Sarastro. The venture was acquired in 1990 by Molecular Dynamics,[29] but the clsm was eventually discontinued. In Germany, Heidelberg Instruments, founded in 1984, developed a clsm which was initially meant for industrial applications, rather than Biology.[30] This instrument was taken over in 1990 by Leica Lasertechnik. Zeiss already hat a non-confocal flying-spot laser scanning microscope on the market which was upgraded to a confocal. A report from 1990,[31] mentioning “some” manufacturers of confocals lists: Sarastro, Technical Instrument, Meridian Instruments, Bio-Rad, Leica, Tracor-Northern and Zeiss.[27]


  1. ^ Pawley JB (editor) (2006). Handbook of Biological Confocal Microscopy (3rd ed.). Berlin: Springer. ISBN 0-387-25921-X. 
  2. ^ Filed in 1957 and granted 1961. US 3013467 
  3. ^ Memoir on Inventing the Confocal Scanning Microscope, Scanning 10 (1988), pp128–138.
  4. ^
  5. ^ "Data Sheet of NanoFocus µsurf spinning disk confocal white light microscope". 
  6. ^ "Data Sheet of Sensofar 'PLu neox' Dual technology sensor head combining confocal and Interferometry techniques, as well as Spectroscopic Reflectometry". 
  7. ^ Vincze L (2005). "Confocal X-ray Fluorescence Imaging and XRF Tomography for Three Dimensional Trace Element Microanalysis". Microscopy and Microanalysis 11 (Supplement 2). doi:10.1017/S1431927605503167. 
  8. ^ Hirschfeld, V. ; Hubner, C.G. (2010). "A sensitive and versatile laser scanning confocal optical microscope for single-molecule fluorescence at 77 K". Review of Scientific Instruments 81, (11) 113705-113705-7, doi:10.1063/1.3499260
  9. ^ Grazioso, F.; Patton, B. R.; Smith, J.M. (2010). "A high stability beam-scanning confocal optical microscope for low temperature operation". Review of Scientific Instruments 81 (9): 093705-4. doi:10.1063/1.3484140
  10. ^ Hans Goldmann (1939). "Spaltlampenphotographie und –photometrie". Ophthalmologica 98 (5/6): 257–270. doi:10.1159/000299716.  Note: Volume 98 is assigned to the year 1939, however on the first page of the article January 1940 is listed as publication date.
  11. ^ a b c d Colin JR Sheppard (3 November 2009). "Confocal Microscopy. The Development of a Modern Microscopy". Imaging & Microscopy. online
  12. ^ a b c Barry R. Masters: Confocal Microscopy And Multiphoton Excitation Microscopy. The Genesis of Live Cell Imaging. SPIE Press, Bellingham, Washington, USA 2006, ISBN 978-0-8194-6118-6, S. 120-121.
  13. ^ Zyun Koana (1942). Journal of the Illumination Engineering Institute 26 (8): 371–385.  Missing or empty |title= (help) The article is available on the website of the journal. The pdf-file labeled „P359 - 402“ is 19020 kilobyte in size and contains also neighboring articles from the same issue. Figure 1b of the article shows the scheme of a confocal transmission beam path.
  14. ^ Naora, Hiroto (1951). "Microspectrophotometry and cytochemical analysis of nucleic acids.". Science 114 (2959): 279–280. PMID 14866220. doi:10.1126/science.114.2959.279. 
  15. ^ Marvin Minsky: Microscopy Apparatus. US Patent 3.013.467, filed 7. November 1957, granted 19. December 1961.
  16. ^ Marvin Minsky (1988). "Memoir on inventing the confocal scanning microscope". Scanning 10 (4): 128–138. doi:10.1002/sca.4950100403. 
  17. ^ Guy Cox: Optical Imaging Techniques in Cell Biology. 1. edition. CRC Press, Taylor & Francis Group, Boca Raton, FL, USA 2006, ISBN 0-8493-3919-7, pages 115-122.
  18. ^ Egger MD, Petrăn M (July 1967). "New reflected-light microscope for viewing unstained brain and ganglion cells". Science 157 (786): 305–7. PMID 6030094. doi:10.1126/science.157.3786.305. 
  19. ^ MOJMÍR PETRÁŇ, MILAN HADRAVSKÝ, M. DAVID EGGER, and ROBERT GALAMBOS (1968). "Tandem-Scanning Reflected-Light Microscope". Journal of the Optical Society of America 58 (5): 661–664. doi:10.1364/JOSA.58.000661. 
  20. ^ Mojmír Petráň, Milan Hadravský: METHOD AND ARRANGEMENT FOR IMPROVING THE RESOLVING, POWER AND CONTRAST. online at Google Patents, filed 4. November 1967, granted 30. June 1970.
  21. ^ Davidovits, P.; Egger, M. D. (1969). "Scanning laser microscope.". Nature 223 (5208): 831. PMID 5799022. doi:10.1038/223831a0. 
  22. ^ Davidovits, P.; Egger, M. D. (1971). "Scanning laser microscope for biological investigations.". Applied optics. 10 (7): 1615–1619. PMID 20111173. doi:10.1364/AO.10.001615. 
  23. ^ Barry R. Masters: Confocal Microscopy And Multiphoton Excitation Microscopy. The Genesis of Live Cell Imaging. SPIE Press, Bellingham, Washington, USA 2006, ISBN 978-0-8194-6118-6, pp. 124-125.
  24. ^ a b c d Shinya Inoué (2006). "Chapter 1: Foundations of Confocal Scanned Imaging in Light Microscopy". In James Pawley. Handbook of Biological Confocal Microscopy (3. ed.). Springer Science and Business Media LLC. pp. 1–19. ISBN 978-0-387-25921-5. 
  25. ^ C.J.R. Sheppard, A. Choudhury: Image Formation in the Scanning Microscope. In: Optica Acta: International Journal of Optics. 24, 1977, S. 1051–1073, doi:10.1080/713819421.
  26. ^ C. Cremer, T. Cremer: Considerations on a laser-scanning-microscope with high resolution and depth of field. In: Microscopica acta. Band 81, Nummer 1, September 1978, S. 31–44, ISSN 0044-376X. PMID 713859.
  27. ^ a b c W. B. Amos, J. G. White: How the confocal laser scanning microscope entered biological research. In: Biology of the cell / under the auspices of the European Cell Biology Organization. Band 95, Nummer 6, September 2003, S. 335–342, ISSN 0248-4900. PMID 14519550. (Review).
  28. ^ Cox, I. J.; Sheppard, C. J. (1983). "Scanning optical microscope incorporating a digital framestore and microcomputer.". Applied optics. 22 (10): 1474. PMID 18195988. doi:10.1364/ao.22.001474. 
  29. ^ Brent Johnson (1 February 1999). "Image Is Everything". The Scientist.  online
  30. ^ website of Heidelberg Instruments GmbH
  31. ^ Diana Morgan (23 July 1990). "Confocal Microscopes Widen Cell Biology Career Horizons". The Scientist.  online