Editing Scanning electron microscope (section)

==Color in SEM==
Electron microscopes do not naturally produce color images. A secondary electron detector produces a single value per [[pixel]] that corresponds to the number of electrons received by the detector during the short period of time when the beam is targeted to the (x,&nbsp;y) pixel position. For each pixel, this single value is represented by a grey level, forming a monochrome image.<ref>{{cite book|last=Burgess|first=Jeremy|title=Under the Microscope: A Hidden World Revealed|year=1987|publisher=CUP Archive|isbn=978-0521399401|url=https://books.google.com/books?id=30A5AAAAIAAJ&pg=PA11|page=11}}</ref> However, several methods can used to get color electron microscopy images.<ref>{{cite web| url = http://viewer.zmags.com/publication/7d4d3b26#/7d4d3b26/34| title = ''Showing your true colors'', 3D and color in electron microscopy in ''Lab News'' magazine}}</ref>

===False color using a single detector===
* On compositional images of flat surfaces (typically BSE):
The easiest way to get color is to replace each grey level with an arbitrary color, using a [[color look-up table]]. This method is known as [[false color]] imaging and can help to distinguish phases of the sample with similar properties or composition.<ref name="Mignot-2018">{{cite journal |last=Mignot|first=Christophe|year=2018 |title=Color (and 3D) for Scanning Electron Microscopy |journal=Microscopy Today |volume=26| issue = 3|pages=12–17 |doi=10.1017/S1551929518000482|doi-access=free}}</ref>

* On textured-surface images:
As an alternative to simply replacing each grey level by a color, a sample observed by an oblique beam allows researchers to create an approximative topography image (see further section [[#Photometric 3D rendering from a single SEM image|"Photometric 3D rendering from a single SEM image"]]). Such topography can then be processed by 3D-rendering algorithms for a more natural rendering of the surface texture.
<gallery widths="220px" heights="160px">

File:Surface of a kidney stone.jpg|Surface of a kidney stone

File:Surface of a kidney stone Re-colorized SEM Image.jpg|The same after re-processing of the color from the estimated topography

File:Discoaster-side-diag-alt hg.jpg|SEM image of a diagenetically altered discoaster

File:Discoaster-side-diag-alt Re-colorized SEM Image.jpg|The same image after similar colorization

</gallery>

===SEM image coloring===
Very often, published SEM images are artificially colored.<ref name="Mignot-2018"/> This may be done for aesthetic effect, to clarify structure or to add a realistic appearance to the sample and generally does not add information about the specimen.<ref>{{cite web|title=Introduction to Electron Microscopy|url=http://www.fei.com/uploadedfiles/documents/content/introduction_to_em_booklet_july_10.pdf|publisher=FEI Company|access-date=12 December 2012|page=15}}</ref>

Coloring may be performed manually with photo-editing software, or semi-automatically with dedicated software using feature-detection or object-oriented segmentation.<ref>{{cite web|title=Next Monday, Digital Surf to Launch Revolutionary SEM Image Colorization|url=http://www.azom.com/news.aspx?newsID=45031|publisher=AZO Materials|access-date=23 January 2016|date=2016-01-22}}</ref>

<gallery widths="220px" heights="160px">
File:Cobaea scandens1-4.jpg|SEM image of ''[[Cobaea scandens]]'' pollen
File:Cobaea scandens colorized SEM image.jpg| The same after semi-automatic coloring. Arbitrary colors help identifying the various elements of the structure.
File:Tradescantia tolmukakarvad ja õietolm.JPG |Colored SEM image of ''[[Tradescantia]]'' pollen and stamens
File:Gold on arsenopyrite SEM image.png |Colored SEM image of native [[gold]] and [[arsenopyrite]] crystal intergrowth
</gallery>

===Color built using multiple electron detectors===
In some configurations more information is gathered per pixel, often by the use of multiple detectors.<ref name="Antonovsky-1984">{{cite journal |last=Antonovsky |first=A. |year=1984 |title=The application of colour to SEM imaging for increased definition |journal=Micron and Microscopica Acta |volume=15 |issue=2 |pages=77–84 |doi=10.1016/0739-6260(84)90005-4}}</ref>

As a common example, secondary electron and backscattered electron detectors are superimposed and a color is assigned to each of the images captured by each detector,<ref name="Danilatos-1986a">{{cite journal |last=Danilatos |first=G.D. |year=1986 |title= Colour micrographs for backscattered electron signals in the SEM|journal=Scanning |volume=9 |issue= 3|pages=8–18|doi=10.1111/j.1365-2818.1986.tb04287.x|s2cid=96315383 }}</ref><ref name="Danilatos-1986b">{{cite journal |last=Danilatos |first=G.D. |year=1986 |title= Environmental scanning electron microscopy in colour|journal=Journal of Microscopy |volume=142 |pages=317–325|doi=10.1002/sca.4950080104|doi-access=free }}</ref> with a result of a combined color image where colors are related to the density of the components. This method is known as density-dependent color SEM (DDC-SEM). Micrographs produced by DDC-SEM retain topographical information, which is  better captured by the secondary electrons detector and combine it to the information about density, obtained by the backscattered electron detector.<ref name="Bertazzo-2013">{{Cite journal
| last1 = Bertazzo | first1 = S.
| last2 = Gentleman | first2 = E.
| last3 = Cloyd | first3 = K. L.
| last4 = Chester | first4 = A. H.
| last5 = Yacoub | first5 = M. H.
| last6 = Stevens | first6 = M. M.
| doi = 10.1038/nmat3627
| title = Nano-analytical electron microscopy reveals fundamental insights into human cardiovascular tissue calcification
| journal = Nature Materials
| volume = 12
| issue = 6
| pages = 576–583
| year = 2013
| pmid = 23603848
| pmc = 5833942
| hdl = 10044/1/21901| bibcode = 2013NatMa..12..576B}}</ref><ref>{{cite journal|last1=Bertazzo|first1=Sergio|last2=Maidment|first2=Susannah C. R.|last3=Kallepitis|first3=Charalambos|last4=Fearn|first4=Sarah|last5=Stevens|first5=Molly M.|last6=Xie|first6=Hai-nan|title=Fibres and cellular structures preserved in 75-million–year-old dinosaur specimens|journal=Nature Communications|date=9 June 2015|volume=6|pages=7352|doi=10.1038/ncomms8352|pmid=26056764|pmc=4468865|bibcode=2015NatCo...6.7352B}}</ref>

<gallery widths="220px" heights="160px">
File:DDC-SEM of calcified particle in cardiac tissue - BW - 1.jpg|DDC-SEM of calcified particle in cardiac tissue - Signal 1: SE|alt=DDC-SEM of calcified particle in cardiac tissue - Signal 1 : SE
File:DDC-SEM_of_calcified_particle_in_cardiac_tissue_-_BW_-_2.jpg| Signal 2: BSE|alt=Signal 2 : BSE
File:DDC-SEM of calcified particle in cardiac tissue - orange.jpg|Colorized image obtained from the two previous. Density-dependent color scanning electron micrograph SEM (DDC-SEM) of cardiovascular calcification, showing in orange a calcium phosphate spherical particle (denser material) and, in green, the extracellular matrix (less dense material)
File:Cardiovascular calcification - Sergio Bertazzo.tif|Same work with a larger view, part of a study on human cardiovascular tissue calcification
</gallery>

===Analytical signals based on generated photons===
Measurement of the energy of photons emitted from the specimen is a common method to get analytical capabilities. Examples are the [[energy-dispersive X-ray spectroscopy]] (EDS) detectors used in elemental analysis and [[cathodoluminescence microscope]] (CL) systems that analyse the intensity and spectrum of electron-induced [[luminescence]] in (for example) geological specimens.  In SEM systems using these detectors it is common to color code these extra signals and superimpose them in a single color image, so that differences in the distribution of the various components of the specimen can be seen clearly and compared. Optionally, the standard secondary electron image can be merged with the one or more compositional channels, so that the specimen's structure and composition can be compared.  Such images can be made while maintaining the full integrity of the original signal data, which is not modified in any way.