Walls, J. R., Sled, J. G., Sharpe, J. & Henkelman, R. M. Correction of artefacts in optical projection tomography. Phys. Med. Biol. 50(19), 4645–4665 (2005).

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The optical setup for BF reconstruction is similar to an OPT system1,37,38 except for two main adjustments: (1) a translation stage is required to scan the sample along the optical axis or to scan the detection optics along the sample; (2) the illumination numerical aperture should match that of the detection: \(NA_{ILL} = NA_{DET}\). This second point is recommended to maximize the resolution of the microscope, which according to Abbe is \(\frac{\lambda }{{NA_{ILL} + NA_{DET} }}\), and consequently to obtain reconstructions with higher-contrast.

Sagittal slice of a transgenic Tg(kdrl:GFP) zebrafish (4 dpf) visualized with bright-field multi-view reconstruction (a). Details of the sample showing a portion of the head (b) and of the zebrafish notochord (c). Minimum intensity projection of the bright-field reconstruction (grey) overlapped with the maximum intensity projection of the LSFM data (green). The bright-field reconstruction shows the whole zebrafish anatomy while LSFM shows the labelled vasculature (d). Transverse section of the sample in the head (e) and tail (f), showing the bright-field reconstruction (grey) and LSFM (green). Scale bars: 100 µm.

Reconstruction of a transverse section of an Arabidopsis thaliana root using Optical Projection Tomography (a), bright-field multi-view reconstruction (b) and bright-field multi-view deconvolution (c). For (c, d), 45 views around 360°, with 8° spacing were used. The presence of spatially variant artifacts in OPT is shown with the blue arrow. The red arrows indicate the thickness of the reconstructed plastic tube far from the rotation center of the OPT reconstruction. Scale bar: 100 µm.

There is no universally accepted definition of the range of infrared radiation. Typically, it is taken to extend from the nominal red edge of the visible spectrum at 780 nm to 1 mm. This range of wavelengths corresponds to a frequency range of approximately 430 THz down to 300 GHz. Beyond infrared is the microwave portion of the electromagnetic spectrum. Increasingly, terahertz radiation is counted as part of the microwave band, not infrared, moving the band edge of infrared to 0.1 mm (3 THz).

Other organisms that have thermoreceptive organs are pythons (family Pythonidae), some boas (family Boidae), the Common Vampire Bat (Desmodus rotundus), a variety of jewel beetles (Melanophila acuminata),[54] darkly pigmented butterflies (Pachliopta aristolochiae and Troides rhadamantus plateni), and possibly blood-sucking bugs (Triatoma infestans).[55] By detecting the heat that their prey emits, crotaline and boid snakes identify and capture their prey using their IR-sensitive pit organs. Comparably, IR-sensitive pits on the Common Vampire Bat (Desmodus rotundus) aid in the identification of blood-rich regions on its warm-blooded victim. The jewel beetle, Melanophila acuminata, locates forest fires via infrared pit organs, where on recently burnt trees, they deposit their eggs. Thermoreceptors on the wings and antennae of butterflies with dark pigmentation, such Pachliopta aristolochiae and Troides rhadamantus plateni, shield them from heat damage as they sunbathe in the sun. Additionally, it's hypothesised that thermoreceptors let bloodsucking bugs (Triatoma infestans) locate their warm-blooded victims by sensing their body heat.[55]

Walls, J. R., Coultas, L., Rossant, J. & Henkelman, R. M. Three-dimensional analysis of vascular development in the mouse embryo. PLoS ONE 3, e2853 (2008).

Remarkably, transmission OPT, which provides bright-field contrast, is used to correct absorption artifacts in Light Sheet Fluorescence Microscopy (LSFM)20,21 and for multimodal reconstruction of the whole specimen’s anatomy22.

Infrared light is also useful for observing the cores of active galaxies, which are often cloaked in gas and dust. Distant galaxies with a high redshift will have the peak portion of their spectrum shifted toward longer wavelengths, so they are more readily observed in the infrared.[10]

After seedling germination and fluorescence inspection, the germinated fluorescent seeds were moved from the plate to the top of FEP tubes filled with gel (prepared accordingly to Candeo et al.,43 and Romano Armada et al.45, using sterilized pliers and without clamping them, so the plantlets could grow inside the filled tubes. The tubes were transferred to a tip box that was finally filled with MS/2 liquid medium without sucrose and sealed to avoid contamination. The mounting procedure and the special illumination and detection configuration of OPT-LSFM allowed the seedlings to be held from the top of the chamber in a vertical position, with the roots growing directly in the jellified medium inside the transparent tubes. To mount the tubes with the plant in the imaging chamber, we used the custom holder reported in Candeo et al.43. When plants were ready to be imaged, we plugged the pipette tip with the tube into the holder, and quickly moved it to the imaging chamber, fixing it on a rotation and translation stage for the sample positioning.

Infrared radiation can be used to remotely determine the temperature of objects (if the emissivity is known). This is termed thermography, or in the case of very hot objects in the NIR or visible it is termed pyrometry. Thermography (thermal imaging) is mainly used in military and industrial applications but the technology is reaching the public market in the form of infrared cameras on cars due to greatly reduced production costs.

These infrared pictures can depict ocean eddies or vortices and map currents such as the Gulf Stream, which are valuable to the shipping industry. Fishermen and farmers are interested in knowing land and water temperatures to protect their crops against frost or increase their catch from the sea. Even El Niño phenomena can be spotted. Using color-digitized techniques, the gray-shaded thermal images can be converted to color for easier identification of desired information.

BF reconstruction can be easily implemented in a multi-view light sheet microscope, complementing the high-resolution fluorescence reconstruction obtained with LSFM. In particular, we acquired images from transgenic Arabidopsis seedlings expressing the Cameleon YC3.640 under the control of AtEXP7 promoter (pEXP7:YC3.6) which directs root hair-specific expression (trichoblast cells) of the fluorescent sensor41. This acquisition shows that by combining LSFM with BF reconstruction the fluorescence can be precisely localized in the context of a single tissue sections (Fig. 4c, d) or in the entire volume (Fig. 4e). It is worth noting that the BF reconstruction is performed with a LED illumination at λ = 530 nm, close to the emission wavelength of GFP, avoiding any chromatic aberration (Fig. 4f).

IR data transmission of audio versions of printed signs is being researched as an aid for visually impaired people through the Remote infrared audible signage project. Transmitting IR data from one device to another is sometimes referred to as beaming.

Candeo, A. et al. Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine. J. Biomed. Opt. 21(5), 056001 (2016).

The pit viper has a pair of infrared sensory pits on its head. There is uncertainty regarding the exact thermal sensitivity of this biological infrared detection system.[52][53]

Sunlight, at an effective temperature of 5,780 K (5,510 °C, 9,940 °F), is composed of near-thermal-spectrum radiation that is slightly more than half infrared. At zenith, sunlight provides an irradiance of just over 1 kW per square meter at sea level. Of this energy, 527 W is infrared radiation, 445 W is visible light, and 32 W is ultraviolet radiation.[13] Nearly all the infrared radiation in sunlight is near infrared, shorter than 4 μm.

Bassi, A., Schmid, B. & Huisken, J. Optical tomography complements light sheet microscopy for in toto imaging of zebrafish development. Development 142, 1016–1020 (2015).

Costa, A., Candeo, A., Fieramonti, L., Valentini, G. & Bassi, A. Calcium dynamics in root cells of Arabidopsis thaliana visualized with selective plane illumination microscopy. PLoS ONE 8, e75646 (2013).

The system required for BF multi-view reconstruction consists in a trans-illumination microscope in which the sample can be rotated over 360° (around the y axis in Fig. 1a) and translated along the optical axis (axis z in Fig. 1a). Like any wide-field microscope, the system presents a limited optical sectioning capability which is a consequence of the so called “missing cone” in the Optical Transfer Function (OTF)33 (Fig. 1b). For this reason, if we acquire a stack of images of the sample at different axial positions, the three-dimensional reconstruction that we obtain will have a limited axial resolution. We observe for example that the transverse section of a sample (an Arabidopsis thaliana root), presents such a poor axial resolution (Fig. 1c, left hand side) that different structures are indistinguishable, hindering any 3D analysis of the sample.

Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, via Fratelli Cervi 93, 20090, Segrate, Italy

Infrared reflectography[48] can be applied to paintings to reveal underlying layers in a non-destructive manner, in particular the artist's underdrawing or outline drawn as a guide. Art conservators use the technique to examine how the visible layers of paint differ from the underdrawing or layers in between (such alterations are called pentimenti when made by the original artist). This is very useful information in deciding whether a painting is the prime version by the original artist or a copy, and whether it has been altered by over-enthusiastic restoration work. In general, the more pentimenti, the more likely a painting is to be the prime version. It also gives useful insights into working practices.[49] Reflectography often reveals the artist's use of carbon black, which shows up well in reflectograms, as long as it has not also been used in the ground underlying the whole painting.

All methods were carried out in accordance with relevant guidelines and regulations. Zebrafish (Danio rerio) were maintained at the zebrafish facility, University of Milan, Via Celoria 26—20133 Milan, Italy (Aut. Prot, n. 295/2012-A—20/12/2012 for the breeding, growth and use of zebrafish, released by the Azienda di Tutela della Salute, ATS Città metropolitana di Milano). All experimental procedures were performed according to the international (EU Directive 2010/63/EU) and national guidelines (Italian decree No 26 of the 4th of March 2014). Embryos were staged and used until 5 days post fertilization, a time windows in which zebrafish is not considered an animal model according to national guidelines (Italian decree No 26 of the 4th of March 2014). All procedures to minimize stress and pain of the embryos were applied. Embryos were anaesthetized with 0.016% tricaine (Ethyl 3-aminobenzoate methanesulfonate salt, Sigma-Aldrich) before proceeding with experimental protocols.

Infrared radiation is emitted or absorbed by molecules when changing rotational-vibrational movements. It excites vibrational modes in a molecule through a change in the dipole moment, making it a useful frequency range for study of these energy states for molecules of the proper symmetry. Infrared spectroscopy examines absorption and transmission of photons in the infrared range.[9]

Infrared is used in night vision equipment when there is insufficient visible light to see.[34] Night vision devices operate through a process involving the conversion of ambient light photons into electrons that are then amplified by a chemical and electrical process and then converted back into visible light.[34] Infrared light sources can be used to augment the available ambient light for conversion by night vision devices, increasing in-the-dark visibility without actually using a visible light source.[34][1]

Correia, T. et al. Accelerated optical projection tomography applied to in vivo imaging of zebrafish. PLoS ONE 10(8), e0136213 (2015).

Infrared radiation is used in industrial, scientific, military, commercial, and medical applications. Night-vision devices using active near-infrared illumination allow people or animals to be observed without the observer being detected. Infrared astronomy uses sensor-equipped telescopes to penetrate dusty regions of space such as molecular clouds, to detect objects such as planets, and to view highly red-shifted objects from the early days of the universe.[10] Infrared thermal-imaging cameras are used to detect heat loss in insulated systems, to observe changing blood flow in the skin, to assist firefighting, and to detect the overheating of electrical components.[11] Military and civilian applications include target acquisition, surveillance, night vision, homing, and tracking. Humans at normal body temperature radiate chiefly at wavelengths around 10 μm. Non-military uses include thermal efficiency analysis, environmental monitoring, industrial facility inspections, detection of grow-ops, remote temperature sensing, short-range wireless communication, spectroscopy, and weather forecasting.

G.C. and A.B designed the experiments. G.C., A.B., C.D., A.Ca, A.F., V.M. and G.V. acquired and analyzed the data, A.Co. and A.P. prepared the samples and developed the imaging protocol. A.B. wrote the manuscript.

Arranz, A. et al. In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster. Sci. Rep. 4, 7325 (2014).

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Köhlerillumination

These divisions are not precise and can vary depending on the publication. The three regions are used for observation of different temperature ranges,[27] and hence different environments in space.

The 1.5-Meter (60 Inch) Tillinghast Telescope is a general purpose visible-light telescope located at the Fred Lawrence Whipple Observatory (FLWO) in southern ...

Andrews, N. et al. Visualising apoptosis in live zebrafish using fluorescence lifetime imaging with optical projection tomography to map FRET biosensor activity in space and time. J. Biophotonics 9(4), 414–424 (2016).

Zebrafish AB strains obtained from the Wilson lab (University College London, London, UK) were maintained at 28 °C on a 14 h light/10 h dark cycle. The zebrafish transgenic Tg(kdrl:GFP) was used for fluorescence imaging. Embryos were collected by natural spawning, staged according to Kimmel and colleagues, and raised at 28 °C in fish water (Instant Ocean, 0.1% Methylene Blue) in Petri dishes, according to established techniques. After 24 hpf, to prevent pigmentation 0.003% 1-phenyl-2-thiourea (PTU, Sigma-Aldrich, Saint Louis, MO, USA) was added to the fish water. Embryos were washed, dechorionated and anaesthetized, with 0.016% tricaine (Ethyl 3-aminobenzoate methanesulfonate salt; Sigma-Aldrich, before acquisitions. During imaging, the fish were restrained in FEP (Fluorinated ethylene propylene) tubes37.

Infrared tracking, also known as infrared homing, refers to a passive missile guidance system, which uses the emission from a target of electromagnetic radiation in the infrared part of the spectrum to track it. Missiles that use infrared seeking are often referred to as "heat-seekers" since infrared (IR) is just below the visible spectrum of light in frequency and is radiated strongly by hot bodies. Many objects such as people, vehicle engines, and aircraft generate and retain heat, and as such, are especially visible in the infrared wavelengths of light compared to objects in the background.[38]

Secondly, to determine the location zC of the rotational axis along the z axis, we adopted an approach typically used in OPT38. We select a single transverse section of the sample (in a certain y location), reconstruct the section assuming different zC values and calculate the contrast of each reconstruction (Fig. 3d–g), as described in Material and Methods. The reconstructed image that has the highest contrast is the closest to the ideal reconstruction, as it is the least blurred. The corresponding zC position is considered to be that of the rotation axis.

In general, objects emit infrared radiation across a spectrum of wavelengths, but sometimes only a limited region of the spectrum is of interest because sensors usually collect radiation only within a specific bandwidth. Thermal infrared radiation also has a maximum emission wavelength, which is inversely proportional to the absolute temperature of object, in accordance with Wien's displacement law. The infrared band is often subdivided into smaller sections, although how the IR spectrum is thereby divided varies between different areas in which IR is employed.

The reconstruction consists in a multi-view fusion of the data acquired at different angles. Data processing was performed in Python; a sample code is available on GitHub (https://github.com/andreabassi78/BrightfieldMultiviewReconstruction).

At each angle, in order to cover the specimen of thickness \(L\), we acquired M images while translating the sample with a step Δz. Since the maximum axial cutoff frequency 33 of the microscope is \(\Delta k_{z} = \frac{{NA^{2} }}{2\lambda n}\), following the Nyquist’s criterion we scanned the sample with an axial step \(\Delta z = \frac{1}{{2 \Delta k_{z} }} = \frac{\lambda n}{{NA^{2} }}\). The number of acquisitions along z is given by \(M = \frac{L}{\Delta z} = \frac{{L \cdot NA^{2} }}{\lambda n}\). We observe that the total number of acquired images \(N_{TOT} = N \cdot M = \frac{2\pi \cdot L \cdot NA }{{ \lambda }}\) scales linearly with the numerical aperture, indicating that the approach is particularly suitable for numerical apertures and magnifications which are between those normally used in OPT and those used in high-resolution optical microscopy.

To accurately reconstruct the data, the position of the rotation axis must be determined at pixel resolution. We propose a straightforward method based on two processing steps to locate the rotation axis, both in x and z, assuming that the latter is parallel to the y axis (as in Fig. 1a).

The onset of infrared is defined (according to different standards) at various values typically between 700 nm and 800 nm, but the boundary between visible and infrared light is not precisely defined. The human eye is markedly less sensitive to light above 700 nm wavelength, so longer wavelengths make insignificant contributions to scenes illuminated by common light sources. Particularly intense near-IR light (e.g., from lasers, LEDs or bright daylight with the visible light filtered out) can be detected up to approximately 780 nm, and will be perceived as red light. Intense light sources providing wavelengths as long as 1,050 nm can be seen as a dull red glow, causing some difficulty in near-IR illumination of scenes in the dark (usually this practical problem is solved by indirect illumination). Leaves are particularly bright in the near IR, and if all visible light leaks from around an IR-filter are blocked, and the eye is given a moment to adjust to the extremely dim image coming through a visually opaque IR-passing photographic filter, it is possible to see the Wood effect that consists of IR-glowing foliage.[29]

NIR and SWIR together is sometimes called "reflected infrared", whereas MWIR and LWIR is sometimes referred to as "thermal infrared".

Infrared heating is also becoming more popular in industrial manufacturing processes, e.g. curing of coatings, forming of plastics, annealing, plastic welding, and print drying. In these applications, infrared heaters replace convection ovens and contact heating.

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On the other hand, the system required for BF reconstruction is also commonly present in multi-view LSFM microscopes, which allow translation and rotation of the specimen. Therefore, we performed our analysis on a LSFM microscope equipped with a Köhler illuminator for trans-illumination. In particular we used a 4× magnification (NA = 0.13) in the detection path: at this magnification and NA, the artifacts given by the diffraction are already present and significantly compromise the standard OPT results (Fig. 2a).

Boot, M. J. et al. In vitro whole-organ imaging: 4D quantification of growing mouse limb buds. Nat. Methods 7, 609–612 (2008).

Recent progress in the design of infrared-sensitive cameras makes it possible to discover and depict not only underpaintings and pentimenti, but entire paintings that were later overpainted by the artist.[50] Notable examples are Picasso's Woman Ironing and Blue Room, where in both cases a portrait of a man has been made visible under the painting as it is known today.

Miao, Q. et al. Resolution improvement in optical projection tomography by the focal scanning method. Opt. Lett. 35, 3363–3365 (2010).

A variety of technologies or proposed technologies take advantage of infrared emissions to cool buildings or other systems. The LWIR (8–15 μm) region is especially useful since some radiation at these wavelengths can escape into space through the atmosphere's infrared window. This is how passive daytime radiative cooling (PDRC) surfaces are able to achieve sub-ambient cooling temperatures under direct solar intensity, enhancing terrestrial heat flow to outer space with zero energy consumption or pollution.[40][41] PDRC surfaces maximize shortwave solar reflectance to lessen heat gain while maintaining strong longwave infrared (LWIR) thermal radiation heat transfer.[42][43] When imagined on a worldwide scale, this cooling method has been proposed as a way to slow and even reverse global warming, with some estimates proposing a global surface area coverage of 1-2% to balance global heat fluxes.[44][45]

On the surface of Earth, at far lower temperatures than the surface of the Sun, some thermal radiation consists of infrared in the mid-infrared region, much longer than in sunlight. Black-body, or thermal, radiation is continuous: it radiates at all wavelengths. Of these natural thermal radiation processes, only lightning and natural fires are hot enough to produce much visible energy, and fires produce far more infrared than visible-light energy.[14]

In the field of climatology, atmospheric infrared radiation is monitored to detect trends in the energy exchange between the Earth and the atmosphere. These trends provide information on long-term changes in Earth's climate. It is one of the primary parameters studied in research into global warming, together with solar radiation.

Bassi, A., Fieramonti, L., D’Andrea, C., Mione, M. & Valentini, G. In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography. J. Biomed. Opt. 16, 100502 (2011).

Infrared radiation is popularly known as "heat radiation",[31] but light and electromagnetic waves of any frequency will heat surfaces that absorb them. Infrared light from the Sun accounts for 49%[32] of the heating of Earth, with the rest being caused by visible light that is absorbed then re-radiated at longer wavelengths. Visible light or ultraviolet-emitting lasers can char paper and incandescently hot objects emit visible radiation. Objects at room temperature will emit radiation concentrated mostly in the 8 to 25 μm band, but this is not distinct from the emission of visible light by incandescent objects and ultraviolet by even hotter objects (see black body and Wien's displacement law).[33]

In the semiconductor industry, infrared light can be used to characterize materials such as thin films and periodic trench structures. By measuring the reflectance of light from the surface of a semiconductor wafer, the index of refraction (n) and the extinction Coefficient (k) can be determined via the Forouhi–Bloomer dispersion equations. The reflectance from the infrared light can also be used to determine the critical dimension, depth, and sidewall angle of high aspect ratio trench structures.

The x location of the center of the rotation axis is found by registering two opposite views projections. The registration is performed using the Python module scikit-image (register_translation) to determine the distance Δx (Fig. 3c).

Strong infrared radiation in certain industry high-heat settings may be hazardous to the eyes, resulting in damage or blindness to the user. Since the radiation is invisible, special IR-proof goggles must be worn in such places.[64]

The main water vapour channel at 6.40 to 7.08 μm can be imaged by some weather satellites and shows the amount of moisture in the atmosphere.

The sensitivity of Earth-based infrared telescopes is significantly limited by water vapor in the atmosphere, which absorbs a portion of the infrared radiation arriving from space outside of selected atmospheric windows. This limitation can be partially alleviated by placing the telescope observatory at a high altitude, or by carrying the telescope aloft with a balloon or an aircraft. Space telescopes do not suffer from this handicap, and so outer space is considered the ideal location for infrared astronomy.

Candeo, A., Doccula, F. G., Valentini, G., Bassi, A. & Costa, A. Light sheet fluorescence microscopy quantifies calcium oscillations in root hairs of Arabidopsis thaliana. Plant Cell Physiol 58(7), 1161–1172 (2017).

Astronomers observe objects in the infrared portion of the electromagnetic spectrum using optical components, including mirrors, lenses and solid state digital detectors. For this reason it is classified as part of optical astronomy. To form an image, the components of an infrared telescope need to be carefully shielded from heat sources, and the detectors are chilled using liquid helium.

Infrared radiation is generally considered to begin with wavelengths longer than visible by the human eye. There is no hard wavelength limit to what is visible, as the eye's sensitivity decreases rapidly but smoothly, for wavelengths exceeding about 700 nm. Therefore wavelengths just longer than that can be seen if they are sufficiently bright, though they may still be classified as infrared according to usual definitions. Light from a near-IR laser may thus appear dim red and can present a hazard since it may actually be quite bright. Even IR at wavelengths up to 1,050 nm from pulsed lasers can be seen by humans under certain conditions.[15][16][17]

Chen, L. et al. Mesoscopic in vivo 3-D tracking of sparse cell populations using angular multiplexed optical projection tomography. Biomed. Opt. Express 6, 1253–1261 (2015).

Three-dimensional imaging of a transgenic pEXP7:YC3.6 Arabidopsis thaliana seedling. Transverse (a) and lateral (b) sections of root tip (mature zone) acquired with bright-field multi-view reconstruction. Transverse (c) and lateral (d) sections acquired with bright-field reconstruction (grey) and LSFM (green). Maximum intensity projection of the LSFM stack, combined with the minimum intensity projection of the bright-field reconstruction (e). Detail of panel e, showing the outgrowing part of the root-hair epidermal cells (f). Three-dimensional rendering of the reconstructed bright-field volume, combined with LSFM. Scale bar: 100 µm.

Trull, A. K. et al. Point spread function based image reconstruction in optical projection tomography. Phys. Med. Biol. 62(19), 7784 (2017).

Infrared vibrational spectroscopy (see also near-infrared spectroscopy) is a technique that can be used to identify molecules by analysis of their constituent bonds. Each chemical bond in a molecule vibrates at a frequency characteristic of that bond. A group of atoms in a molecule (e.g., CH2) may have multiple modes of oscillation caused by the stretching and bending motions of the group as a whole. If an oscillation leads to a change in dipole in the molecule then it will absorb a photon that has the same frequency. The vibrational frequencies of most molecules correspond to the frequencies of infrared light. Typically, the technique is used to study organic compounds using light radiation from the mid-infrared, 4,000–400 cm−1. A spectrum of all the frequencies of absorption in a sample is recorded. This can be used to gain information about the sample composition in terms of chemical groups present and also its purity (for example, a wet sample will show a broad O-H absorption around 3200 cm−1). The unit for expressing radiation in this application, cm−1, is the spectroscopic wavenumber. It is the frequency divided by the speed of light in vacuum.

Infrared (IR; sometimes called infrared light) is electromagnetic radiation (EMR) with wavelengths longer than that of visible light but shorter than microwaves. The infrared spectral band begins with waves that are just longer than those of red light (the longest waves in the visible spectrum), so IR is invisible to the human eye. IR is generally understood to include wavelengths from around 750 nm (400 THz) to 1 mm (300 GHz).[1][2] IR is commonly divided between longer-wavelength thermal IR, emitted from terrestrial sources, and shorter-wavelength IR or near-IR, part of the solar spectrum.[3] Longer IR wavelengths (30–100 μm) are sometimes included as part of the terahertz radiation band.[4] Almost all black-body radiation from objects near room temperature is in the IR band. As a form of electromagnetic radiation, IR carries energy and momentum, exerts radiation pressure, and has properties corresponding to both those of a wave and of a particle, the photon.[5]

The discovery of infrared radiation is ascribed to William Herschel, the astronomer, in the early 19th century. Herschel published his results in 1800 before the Royal Society of London. Herschel used a prism to refract light from the sun and detected the infrared, beyond the red part of the spectrum, through an increase in the temperature recorded on a thermometer. He was surprised at the result and called them "Calorific Rays".[65][66] The term "infrared" did not appear until late 19th century.[67] An earlier experiment in 1790 by Marc-Auguste Pictet demonstrated the reflection and focusing of radiant heat via mirrors in the absence of visible light.[68]

A pyrgeometer is utilized in this field of research to perform continuous outdoor measurements. This is a broadband infrared radiometer with sensitivity for infrared radiation between approximately 4.5 μm and 50 μm.

Cheddad, A., Svensson, C., Sharpe, J., Georgsson, F. & Ahlgren, U. Image processing assisted algorithms for optical projection tomography. IEEE Trans. Med. Imaging 31(1), 1–15 (2012).

McGinty, J. et al. In vivo fluorescence lifetime optical projection tomography. Biomed. Opt. Express 2(5), 1340–1350 (2011).

Swoger, J., Verveer, P., Greger, K., Huisken, J. & Stelzer, E. H. Multi-view image fusion improves resolution in three-dimensional microscopy. Opt. Express 15, 8029–8042 (2007).

Bryson-Richardson, R. & Currie, P. Optical projection tomography for spatio-temporal analysis in the zebrafish. Methods Cell Biol. 76, 37–50 (2004).

In summary we have shown that three-dimensional reconstructions of unstained samples can be achieved in multi-view microscopes, with isotropic resolution, typical of OPT, but without the diffraction artifacts that affect OPT reconstruction. The bright-field multi-view reconstruction provides a comprehensive picture of zebrafish and Arabidopsis thaliana anatomy, including organs that are usually not labelled and therefore not observable. The bright-field contrast nicely complements the fluorescence contrast observable with LSFM, allowing correlative fluorescent protein expression and anatomical visualization.

Fieramonti, L. et al. Time-gated optical projection tomography allows visualization of adult zebrafish internal structures. PLoS ONE 7(11), e50744 (2012).

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Then, stacks acquired at the different angles are resliced into planes (xz) which are orthogonal to the rotation axis. The z location of the center of rotation is found by maximizing the contrast of the reconstruction at different possible zC. The contrast is calculated as the energy (sum) of all the frequency components obtained by numerically Fourier transforming (fft2 function in the Python module numpy) the reconstruction, excluding the DC component.

Darkfieldmicroscopy

As described and characterized by Trull et al.24, the diffraction of light in OPT causes space-variant tangential blurring that increases with the distance from the rotation axis. We clearly observe these artifacts when imaging structures that are just hundreds of microns away from the rotation axis. This effect is shown in the completely distorted reconstruction (Fig. 2a, blue arrow) of a root hair of Arabidopsis thaliana, which is c.a 200 µm away from the rotation axis (located at the center of the OPT reconstructed section in Fig. 2a). In Fig. 2, the sample was embedded in a tube (see Material and Methods) that is visible in the OPT reconstruction due to the presence of a small amount of scattering which causes light attenuation. The size of the tube can be used as a benchmark to assess the presence of space-variant blurring. We observe that the higher the distance from the center of rotation, the more blurred the border of the tube is in the OPT reconstruction. When applying the multi-view approach, the sample is reconstructed correctly in the entire field of view, avoiding the diffraction artifacts (Fig. 2b). However, as expected, by simply overlapping (sum) the views acquired at different angles, the image is overall blurred. In order to increase the quality of the reconstruction we used a deconvolution approach based on the Wiener or Lucy Richardson methods (see Material and Methods). In this way, the contrast and resolution are significantly improved leading to the observation of the Arabidopsis section at single cell detail (Fig. 2c). This improvement comes at the expense of higher noise, and in order to fully exploit the capabilities of the method a systematic study on deconvolution and regularization should still be carried out. It is worth noting that in case of highly diffusive samples the technique would be able to reconstruct only the outermost part of the specimen with artifacts given by the diffusion of light. Therefore, the method should be applied to translucent samples (as it is the case for zebrafish embryos and Arabidopsis roots), chemically cleared samples, or it should be combined with more advanced methods to reduce the effect of diffusion34,35,39.

Experimental setup for multi-view bright-field reconstruction: an LED (530 nm) illuminates the sample, the transmitted light is collected by a detection optical system and a camera. The sample is mounted on a translation and a rotation stage to be scanned and rotated around 360°. A stack of images is acquired in each angular position while scanning the sample (a). Scheme of the Optical Transfer Function of the microscope (b, upper panel). Acquiring multiple views is equivalent to rotating the OTF and sampling different spatial frequencies (b, lower panel). Reconstruction of the transverse section of a sample (Arabidopsis thaliana) using a single view (0°), 10 views (covering 60° in total) and 60 views (covering 360°), each with a spacing of 6°. The illumination and detection numerical aperture is NA = 0.13 (c). Scale bar: 50 µm.

OCC, DX, Distribution Series, 4-Strand, 900um Tight Buffered, Indoor/Outdoor, Chemical Resistant OFNP Plenum Rated, 9/125, Singlemode Bend ...

Bassi, A., Fieramonti, L., D’Andrea, C., Valentini, G. & Mione, M. In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography. J. Biomed. Opt. 16(10), 100502 (2011).

Clouds with high and cold tops, such as cyclones or cumulonimbus clouds, are often displayed as red or black, lower warmer clouds such as stratus or stratocumulus are displayed as blue or grey, with intermediate clouds shaded accordingly. Hot land surfaces are shown as dark-grey or black. One disadvantage of infrared imagery is that low clouds such as stratus or fog can have a temperature similar to the surrounding land or sea surface and do not show up. However, using the difference in brightness of the IR4 channel (10.3–11.5 μm) and the near-infrared channel (1.58–1.64 μm), low clouds can be distinguished, producing a fog satellite picture. The main advantage of infrared is that images can be produced at night, allowing a continuous sequence of weather to be studied.

Kohler illumination is a method of specimen lighting used in professional standard transmitted or reflected light microscopes. It was first described by August ...

It was long known that fires emit invisible heat; in 1681 the pioneering experimenter Edme Mariotte showed that glass, though transparent to sunlight, obstructed radiant heat.[6][7] In 1800 the astronomer Sir William Herschel discovered that infrared radiation is a type of invisible radiation in the spectrum lower in energy than red light, by means of its effect on a thermometer.[8] Slightly more than half of the energy from the Sun was eventually found, through Herschel's studies, to arrive on Earth in the form of infrared. The balance between absorbed and emitted infrared radiation has an important effect on Earth's climate.

In order to obtain optical sectioning, we acquired multiple views of the specimen separated by an angle Δα and at each angle we collected a stack of images with sampling steps Δz. The different stacks were fused together to create a single reconstruction of the sample. We estimated the required number N of views by looking at the system OTF (Fig. 1b). Considering that, in paraxial approximation, the angle θ subtended by the OTF is approximately the system numerical aperture \(NA = n sin\theta \approx n\theta\) (where n is the index of refraction), we chose to acquire the views at an angle step of \(\Delta \alpha = \theta\) so that the maximum of each OTF overlapped with the minimum of the adjacent one. In this case, the number of acquired views resulted in \(N = \frac{2\pi }{{\Delta \alpha }} = \frac{2\pi n}{{NA}}\). One could exploit the symmetry of the OTF and acquire only \(\frac{N}{2}\) views around 180°, however in presence of scattering34,35,36 the acquisition of the sample around full 360° provided a more resolved reconstruction.

Sharpe, J. et al. Optical projection tomography as a tool for 3D microscopy and gene expression studies. Science 296, 541–545 (2002).

Near-infrared light, or photobiomodulation, is used for treatment of chemotherapy-induced oral ulceration as well as wound healing. There is some work relating to anti-herpes virus treatment.[62] Research projects include work on central nervous system healing effects via cytochrome c oxidase upregulation and other possible mechanisms.[63]

A hyperspectral image is a "picture" containing continuous spectrum through a wide spectral range at each pixel. Hyperspectral imaging is gaining importance in the field of applied spectroscopy particularly with NIR, SWIR, MWIR, and LWIR spectral regions. Typical applications include biological, mineralogical, defence, and industrial measurements.

In infrared photography, infrared filters are used to capture the near-infrared spectrum. Digital cameras often use infrared blockers. Cheaper digital cameras and camera phones have less effective filters and can view intense near-infrared, appearing as a bright purple-white color. This is especially pronounced when taking pictures of subjects near IR-bright areas (such as near a lamp), where the resulting infrared interference can wash out the image. There is also a technique called 'T-ray' imaging, which is imaging using far-infrared or terahertz radiation. Lack of bright sources can make terahertz photography more challenging than most other infrared imaging techniques. Recently T-ray imaging has been of considerable interest due to a number of new developments such as terahertz time-domain spectroscopy.

Mayer, J., Robert-Moreno, A., Sharpe, J. & Swoger, J. Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM. Light Sci. Appl. 7, 70 (2018).

This approach assumes that the rotation axis is perfectly perpendicular to the optical axis of the detection objective. If this is not the case, we suggest to repeat the procedure at two or more y locations and then linearly interpolate the values of xC and zC for all the considered y values.

Using BF reconstruction, we managed to acquire a large volume of the biological sample in a single measurement. We tested the method in vivo with Arabidopsis thaliana and zebrafish (Danio rerio) samples. In the root of Arabidopsis seedlings, the reconstruction can be extended to a large portion of the root including the root hairs, which are long tubular-shaped outgrowths from root epidermal cells (Fig. 4 and Supplementary Fig. 3). One key feature of the technique is to provide isotropic resolution over the entire reconstructed volume. In addition, the method is label-free, since the BF reconstruction is based on trans-illumination. In living samples, the contrast is given by the attenuation of light, primarily due to scattering and absorption. Therefore, while on the one hand the staining is not required for imaging, on the other hand, since low-power light sources are used for trans-illumination, the measurements induce minimum photo-toxicity to the biological sample. These features make the technique an ideal tool for assessing the anatomy of the sample in-vivo.

Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle ricerche, piazza Leonardo da Vinci 32, 20133, Milan, Italy

Alanentalo, T. et al. Tomographic molecular imaging and 3D quantification within adult mouse organs. Nat. Methods 4, 31–33 (2007).

First, two stacks of images are acquired at opposite angles (e.g. 0° and 180°) and the two corresponding projections are created (mean intensity projection or minimum intensity projection, as shown in Fig. 3a, b). One of the two projections is flipped along the x axis and translated to overlap to the other using an image registration algorithm: in order to overlap the two images, the second projection is translated by a distance Δx (Fig. 3c). The location xC of the rotation axis is then calculated as the sum of semi-width of the image and the distance Δx/2.

Lee, K. et al. Visualizing plant development and gene expression in three dimensions using optical projection tomography. Plant Cell 18, 2145–2156 (2006).

Infrared cleaning is a technique used by some motion picture film scanners, film scanners and flatbed scanners to reduce or remove the effect of dust and scratches upon the finished scan. It works by collecting an additional infrared channel from the scan at the same position and resolution as the three visible color channels (red, green, and blue). The infrared channel, in combination with the other channels, is used to detect the location of scratches and dust. Once located, those defects can be corrected by scaling or replaced by inpainting.[47]

The sample is rotated by \(\Delta \alpha\) and the previous points are repeated for multiview acquisition. Typically the angle \(\Delta \alpha\) is chosen so to have a full 360° rotation after N + 1 rotation steps.

Measurements of zebrafish embryos demonstrate that the whole organism can be acquired in a single experiment. Again, the technique offers the possibility to observe several organs (e.g. notochord, yolk, eye, brain) in single sections (Fig. 5a–c and Supplementary Fig. 4) and within the entire sample anatomy. The use of 4 days post fertilization (dpf) transgenic VEGFR2:GFP zebrafish embryos that express green fluorescent protein under the control of the vascular endothelial promoter VEGFR2/KDR [Tg(kdrl:GFP)]42, confirms that the combination of LSFM and BF reconstruction is a suitable tool to localize a sparse fluorescence signal in the tissue (Fig. 5d–f).

Near-infrared is the region closest in wavelength to the radiation detectable by the human eye. mid- and far-infrared are progressively further from the visible spectrum. Other definitions follow different physical mechanisms (emission peaks, vs. bands, water absorption) and the newest follow technical reasons (the common silicon detectors are sensitive to about 1,050 nm, while InGaAs's sensitivity starts around 950 nm and ends between 1,700 and 2,600 nm, depending on the specific configuration). No international standards for these specifications are currently available.

2022228 — Plane-polarized light is the light in which the electrical field vibrates only on one plane. see also optical rotation

The use of infrared light and night vision devices should not be confused with thermal imaging, which creates images based on differences in surface temperature by detecting infrared radiation (heat) that emanates from objects and their surrounding environment.[35][8]

Widefield microscope

Multimodal acquisition (bright-field/fluorescence) is performed alternating the LED (for trans-illumination) and the laser (for LSFM). After each axial scan required for bright-field acquisition, a second axial scan is repeated for LSFM acquisition. To this end two custom-made mechanical shutters are used to alternate the illuminations.

Fauver, M. et al. Three-dimensional imaging of single isolated cell nuclei using optical projection tomography. Opt. Express 13, 4210–4223 (2005).

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

van der Horst, J. & Kalkman, J. Image resolution and deconvolution in optical tomography. Opt. Express 24(21), 24460–24472 (2016).

Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J. & Stelzer, E. H. Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305, 1007–1009 (2004).

Free-space optical communication using infrared lasers can be a relatively inexpensive way to install a communications link in an urban area operating at up to 4 gigabit/s, compared to the cost of burying fiber optic cable, except for the radiation damage. "Since the eye cannot detect IR, blinking or closing the eyes to help prevent or reduce damage may not happen."[46]

Optical Projection Tomography (OPT) is a powerful three-dimensional imaging technique used for the observation of millimeter-scaled biological samples, compatible with bright-field and fluorescence contrast. OPT is affected by spatially variant artifacts caused by the fact that light diffraction is not taken into account by the straight-light propagation models used for reconstruction. These artifacts hinder high-resolution imaging with OPT. In this work we show that, by using a multiview imaging approach, a 3D reconstruction of the bright-field contrast can be obtained without the diffraction artifacts typical of OPT, drastically reducing the amount of acquired data, compared to previously reported approaches. The method, purely based on bright-field contrast of the unstained sample, provides a comprehensive picture of the sample anatomy, as demonstrated in vivo on Arabidopsis thaliana and zebrafish embryos. Furthermore, this bright-field reconstruction can be implemented on practically any multi-view light-sheet fluorescence microscope without complex hardware modifications or calibrations, complementing the fluorescence information with tissue anatomy.

Kumar, V., Chyou, S., Stein, J. V. & Lu, T. T. Optical projection tomography reveals dynamics of HEV growth after immunization with protein plus CFA and features shared with HEVs in acute autoinflammatory lymphadenopathy. Front. Immunol. 3, 282 (2012).

A Köhler illuminator is used for trans-illumination of the sample. The light source is a LED (Thorlabs M530L2) emitting at 530 nm. The transmitted light is collected by a microscope objective lens (Nikon M = 4×, NADET = 0.13 or Olympus M = 10×, NADET = 0.3) and tube lens to form the image of the sample on a sCMOS camera (Hamamatsu, Flash 4.0). A long pass filter at 500 nm (Thorlabs FEL0500) is placed between the objective lens and the tube lens, suitable for the collection of 530 nm illumination and also for GFP fluorescence detection. The numerical aperture of the Köhler illuminator is matched to that of the detection (NAILL = NADET). The sample is immersed in a cuvette filled with medium from the top, and is translated along the z-axis with a linear stage (Physik Instrument, M-404.1PD) and rotated with a rotation stage (Physik Instrument M-660.55). A manual translator (Thorlabs, ST1XY-S/M) is mounted on the rotation stage to move the sample on the xz plane and position it in the proximity of the rotation axis. This ensures that the specimen is within the field of view at all the acquisition angles. The sample holder and the pre-alignment protocol are described in Bassi et al.22. The experiments are performed with a custom-made light sheet microscope46. For LSFM illumination, a solid-state laser emitting at 473 nm (CNI, MBL-FN-473) is used. The laser beam is expanded to a diameter of 7 mm and split into two portions in order to illuminate the sample from opposite sides: two cylindrical lenses (Thorlabs, LJ1703RM-A, f = 75 mm) are used to create a light sheet made by two counter-propagating beams across the sample. The illumination is perpendicular to the detection path, with the light-sheet formed in the focal plane of the detection objective lens. LSFM and bright-field reconstruction share the same detection system and the acquisition protocol is the same for the two modalities.

In this case, the theoretical number of acquired views is \(N = \frac{2\pi n}{{NA}} \approx 48\) and the theoretical axial step is \(\Delta z = \frac{\lambda n}{{NA^{2} }} \approx 30 \;\upmu {\text{m}}\) (here λ = 530 nm). For a sample of thickness L = 300 µm the number of steps results in M ≈ 10. The results of the reconstruction performed for different values of N and M (Supplementary Fig. 1) confirm that the theoretical values are a good estimate: above N = 45 and M = 10 the increase in image contrast is negligible. The number of required views is therefore an order of magnitude smaller than the number of projections in standard OPT. Yet, the total amount of data remains practically constant because for each view a stack of images is required, but overall the acquisition time is comparable to that of standard OPT (1–5 min per sample).

Armada, N. R. et al. In vivo light sheet fluorescence microscopy of calcium oscillations in Arabidopsis thaliana. Methods Mol. Biol. Calcium Signal. 10, 87–101 (2019).

Once the rotation axis is defined we process each plane independently, following an approach that has been proven to work properly in multi-view reconstruction of LSFM data in zebrafish47 and offers the possibility to be accelerated using graphics processing units (GPU), potentially providing the results in real time. Each xz plane is rotated around (xC, zC), by its angle view, and summed to the other views. In total, N different views are summed (N is the number of acquired image stacks around 360°) and the resulting image is divided by N. This mean image is the reconstructed plane. If deconvolution is applied, each xz plane is de-convolved before the sum. For deconvolution we used the theoretical point spread function (PSF) of the microscope. This is generated considering the numerical aperture of the lens, creating the corresponding Ewald sphere33, and calculating the absolute value squared of its 3D Fourier transform. For plane by plane processing, a two dimensional PSF is extracted from its three dimensional counterpart by slicing it in its central section. Deconvolution is then performed using the Wiener or Lucy Richardson filtering in the Python package scikit-image.

Here we show that the Bright-Field (BF) contrast can be efficiently reconstructed in 3D by adopting a multi-view image processing method: we propose to fuse three-dimensional image data sets of the sample acquired at multiple angles into a single reconstruction. Each data set consists of a stack of bright-field images acquired by scanning the sample along the optical axis. The method requires the acquisition of a reduced number of angles and eliminates the diffraction artifacts, still providing isotropic resolution and 3D reconstruction of unlabeled samples. The reconstruction is not based on a back-projection algorithm, it uses a multiview fusion approach, that is frequently used in fluorescence imaging30. Here we describe how to apply this approach to reconstruct the BF contrast and we identify the optimal parameters for reconstruction as a function of the spatial and angular sampling. We present in-vivo data of Arabidopsis thaliana and zebrafish (Danio rerio) in order to demonstrate that the approach allows one to observe the whole anatomy of unstained organisms. Finally, we show that, with small modification of the hardware, BF reconstruction can be readily implemented in any multi-view Light Sheet Fluorescence Microscope (LSFM)31,32, obtaining multimodal (bright-field and fluorescence) acquisitions with the same instrument.

The International Commission on Illumination (CIE) recommended the division of infrared radiation into the following three bands:[23][24]

3X (75mm wide) + 45X (22mm wide) Magnifying Lenses · 3 LED light bulbs: 2 for larger lens, 1 for smaller lens · Enables seeing fine-cut details in vinyl graphics ...

Nagai, T., Yamada, S., Tominaga, T., Ichikawa, M. & Miyawaki, A. Expanded dynamic range of fluorescent indicators for Ca2+ by circularly permuted yellow fluorescent proteins. Proc. Natl. Acad. Sci. 101(29), 10554–10559 (2004).

In optical communications, the part of the infrared spectrum that is used is divided into seven bands based on availability of light sources, transmitting/absorbing materials (fibers), and detectors:[30]

Three-dimensional optical imaging techniques are essential tools for observing the structure and understanding the function of biological samples. Among them Optical Projection Tomography (OPT), is well suited to study specimens ranging in size from hundreds of microns to a centimeter1. OPT is often considered the optical analogous of X-ray Computed Tomography (CT), performing tomographic optical imaging of three dimensional samples with transmitted and fluorescent light. OPT can be used in a number of different applications with specimens that include embryos2,3, mouse organs4,5,6 and plants7. At the same time novel OPT configurations have been presented to achieve fast acquisition8,9,10, to reconstruct the fluorescence lifetime and Förster resonance energy transfer contrast11,12, to obtain the contrast from blood flow13,14,15,16. In parallel, advanced recontruction algorithms have constantly been developed17,18,19.

IR data transmission is also employed in short-range communication among computer peripherals and personal digital assistants. These devices usually conform to standards published by IrDA, the Infrared Data Association. Remote controls and IrDA devices use infrared light-emitting diodes (LEDs) to emit infrared radiation that may be concentrated by a lens into a beam that the user aims at the detector. The beam is modulated, i.e. switched on and off, according to a code which the receiver interprets. Usually very near-IR is used (below 800 nm) for practical reasons. This wavelength is efficiently detected by inexpensive silicon photodiodes, which the receiver uses to convert the detected radiation to an electric current. That electrical signal is passed through a high-pass filter which retains the rapid pulsations due to the IR transmitter but filters out slowly changing infrared radiation from ambient light. Infrared communications are useful for indoor use in areas of high population density. IR does not penetrate walls and so does not interfere with other devices in adjoining rooms. Infrared is the most common way for remote controls to command appliances. Infrared remote control protocols like RC-5, SIRC, are used to communicate with infrared.

Search of the rotation axis. Minimum intensity projection (each pixel shows the minimum value of the stack calculated along the z direction) of the stack acquired at the angle 0° (a). Minimum intensity projection of the stack acquired at the angle 180° (b). The image shown in b, is flipped horizontally and translated to overlap the image in a. The distance Δx/2 indicates the position of the rotation axis from the image center, along the horizontal direction (c). Blurring artifacts arising from incorrectly identified axial position of the rotational axis zC (d–f). The contrast of a series of test reconstructions (g) has a maximum at the position corresponding to the correct rotational axis (zC = 0). Scale bars: 50 µm.

Weather satellites equipped with scanning radiometers produce thermal or infrared images, which can then enable a trained analyst to determine cloud heights and types, to calculate land and surface water temperatures, and to locate ocean surface features. The scanning is typically in the range 10.3–12.5 μm (IR4 and IR5 channels).

The project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 871124.

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Similar uses of infrared are made by conservators and scientists on various types of objects, especially very old written documents such as the Dead Sea Scrolls, the Roman works in the Villa of the Papyri, and the Silk Road texts found in the Dunhuang Caves.[51] Carbon black used in ink can show up extremely well.

Criticalillumination

Hyung-Taeg, C. & Cosgrove, D. J. Regulation of root hair initiation and expansin gene expression in Arabidopsis. Plant Cell 14(12), 3237–3253 (2002).

The idea behind OPT is to acquire images (or projections) of the sample from different orientations. Similarly to X-ray CT the sample is then reconstructed using a back-projection algorithm23. However, this algorithm assumes that the light beam propagates straight through the sample: in X-ray CT the straight propagation is given by the high frequency of the radiation, whereas in OPT we can consider a straight propagation of light only within the depth of field of the system. Since the depth of field scales with the inverse of the second power of the Numerical Aperture (NA), the assumption is valid only at low NA (c.a < 0.1) which typically corresponds to a low magnification (1×, 2×). At higher NAs, artifacts due to the diffraction of light are present24. One way to attenuate these artifacts consists in limiting the NA of the microscope (e.g. by inserting a diaphragm at the back focal plane of the detection objective), but this also limits the resolution. Another way to mitigate this effect is to incorporate a spatially variant deconvolution in the reconstruction algorithm24,25. To drastically remove the diffraction artifact, some methods based on the extension of the depth of field have been proposed21,26,27,28. For each projection, the sample is scanned at different positions (up to 100) along the optical axis, and the acquired stack of images is merged into a single entirely focused projection29. Yet, this come at the expenses of the number of acquired images, since the process must be repeated for each projection (up to 1,000 angles within 360° rotation).

Calisesi, G., Candeo, A., Farina, A. et al. Three-dimensional bright-field microscopy with isotropic resolution based on multi-view acquisition and image fusion reconstruction. Sci Rep 10, 12771 (2020). https://doi.org/10.1038/s41598-020-69730-4

The concept of emissivity is important in understanding the infrared emissions of objects. This is a property of a surface that describes how its thermal emissions deviate from the ideal of a black body. To further explain, two objects at the same physical temperature may not show the same infrared image if they have differing emissivity. For example, for any pre-set emissivity value, objects with higher emissivity will appear hotter, and those with a lower emissivity will appear cooler (assuming, as is often the case, that the surrounding environment is cooler than the objects being viewed). When an object has less than perfect emissivity, it obtains properties of reflectivity and/or transparency, and so the temperature of the surrounding environment is partially reflected by and/or transmitted through the object. If the object were in a hotter environment, then a lower emissivity object at the same temperature would likely appear to be hotter than a more emissive one. For that reason, incorrect selection of emissivity and not accounting for environmental temperatures will give inaccurate results when using infrared cameras and pyrometers.

Thermal infrared hyperspectral imaging can be similarly performed using a thermographic camera, with the fundamental difference that each pixel contains a full LWIR spectrum. Consequently, chemical identification of the object can be performed without a need for an external light source such as the Sun or the Moon. Such cameras are typically applied for geological measurements, outdoor surveillance and UAV applications.[37]

Chen, L. et al. Remote focal scanning optical projection tomography with an electrically tunable lens. Biomed. Opt. Express 5(10), 3367–3375 (2014).

The infrared portion of the spectrum has several useful benefits for astronomers. Cold, dark molecular clouds of gas and dust in our galaxy will glow with radiated heat as they are irradiated by imbedded stars. Infrared can also be used to detect protostars before they begin to emit visible light. Stars emit a smaller portion of their energy in the infrared spectrum, so nearby cool objects such as planets can be more readily detected. (In the visible light spectrum, the glare from the star will drown out the reflected light from a planet.)

The most common photometric system used in astronomy allocates capital letters to different spectral regions according to filters used; I, J, H, and K cover the near-infrared wavelengths; L, M, N, and Q refer to the mid-infrared region. These letters are commonly understood in reference to atmospheric windows and appear, for instance, in the titles of many papers.

The sample is translated along the optical axis and images are continuously acquired by the camera. The velocity of the linear stage is synchronized with the acquisition so that every captured image corresponds to a linear step of Δz.

The C-band is the dominant band for long-distance telecommunications networks. The S and L bands are based on less well established technology, and are not as widely deployed.

Heat is energy in transit that flows due to a temperature difference. Unlike heat transmitted by thermal conduction or thermal convection, thermal radiation can propagate through a vacuum. Thermal radiation is characterized by a particular spectrum of many wavelengths that are associated with emission from an object, due to the vibration of its molecules at a given temperature. Thermal radiation can be emitted from objects at any wavelength, and at very high temperatures such radiation is associated with spectra far above the infrared, extending into visible, ultraviolet, and even X-ray regions (e.g. the solar corona). Thus, the popular association of infrared radiation with thermal radiation is only a coincidence based on typical (comparatively low) temperatures often found near the surface of planet Earth.

Fieramonti, L. et al. Quantitative measurement of blood velocity in zebrafish with optical vector field tomography. J. Biophotonics 8(1–2), 52–59 (2015).

Cross, L. M., Cook, M. A., Lin, S., Chen, J. N. & Rubinstein, A. L. Rapid analysis of angiogenesis drugs in a live fluorescent zebrafish assay. Arterioscler. Thromb. Vasc. Biol. 23, 911–912 (2003).

Although near-infrared vision (780–1,000 nm) has long been deemed impossible due to noise in visual pigments,[57] sensation of near-infrared light was reported in the common carp and in three cichlid species.[57][58][59][60][61] Fish use NIR to capture prey[57] and for phototactic swimming orientation.[61] NIR sensation in fish may be relevant under poor lighting conditions during twilight[57] and in turbid surface waters.[61]

These spectra represent the output of the OSL2B bulb installed in the OSL2 light source (blue line) and the OSL2BIR bulb installed in the OSL2IR light source ( ...

Thermographic cameras detect radiation in the infrared range of the electromagnetic spectrum (roughly 9,000–14,000 nm or 9–14 μm) and produce images of that radiation. Since infrared radiation is emitted by all objects based on their temperatures, according to the black-body radiation law, thermography makes it possible to "see" one's environment with or without visible illumination. The amount of radiation emitted by an object increases with temperature, therefore thermography allows one to see variations in temperature (hence the name).

Arabidopsis thaliana seedling preparation was carried out accordingly to Candeo et al.43,44. and Romano Armada et al.45. Briefly, seeds of Arabidopsis thaliana Col-0 transformed with pEXP7:YC3.6 were surface sterilized by vapour-phase sterilization and plated on MS/2 medium supplemented with 0.1% (w/v) sucrose, 0.05% (w/v) MES, pH 5.8 adjusted with KOH and solidified with 0.8% (w/v) plant agar (Duchefa, The Netherlands). After stratification at 4 °C in the dark for 2–3 days, seeds were transferred to the growth chamber with 16/8 h cycles of light (70 µmol m−2 s−1) at 24 °C.

Infrared radiation can be used as a deliberate heating source. For example, it is used in infrared saunas to heat the occupants. It may also be used in other heating applications, such as to remove ice from the wings of aircraft (de-icing).[39] Infrared radiation is used in cooking, known as broiling or grilling. One energy advantage is that the IR energy heats only opaque objects, such as food, rather than the air around them.[25]

Mayer, J. et al. OPTiSPIM: integrating optical projection tomography in light sheet microscopy extends specimen characterization to non-fluorescent contrasts. Opt. Lett. 39(4), 1053–1056 (2014).

Infrared lasers are used to provide the light for optical fiber communications systems. Wavelengths around 1,330 nm (least dispersion) or 1,550 nm (best transmission) are the best choices for standard silica fibers.

The technique performs well also at higher NA. An example of reconstruction at NA = 0.3 with 10× magnification is shown in Supplementary Fig. 2. Here the diffraction artifacts in standard OPT are much stronger and a strategy for extending the depth of field22,27,28 would be in any case required. However, the focus of the present paper is to image an entire sample in a single measurement, which is demonstrated at lower magnification.