question: If an atom is so profoundly tiny that only recently we could actually "see" them, with even SEM's being nowhere near powerful enough, how were we able to confirm sub-elementary particles such as Quarks existed, aside from inferring their existence via mathematics? Can we "see" them now, too?
comment: Quarks pop out of the math. They are far, far too small to be probed ("seen"). In fact, quarks exist only in the sense that the Standard Model requires them, but if the SM is supplanted by another, more complete theory that didn't include quarks (or, put more directly, supplanted by a theory that made better predictions than the SM or made both all the predictions the SM can as well as additional predictions it can't and such a theory did not include quarks), then the existence of quarks would be seen as unnecessary and quarks would no longer "exist."
passages: Drawing on Rutherford's groundbreaking experiments in the early years of the 20th century, ideas for detecting quarks were formulated. Rutherford had proven that atoms had a small, massive, charged nucleus at their centre by firing alpha particles at atoms of gold. Most had gone through with little or no deviation, but a few were deflected through large angles or came right back. This suggested that atoms had internal structure and a lot of empty space.
   BULLET::::- The quarks, which were massive particles that carried fractional electric charges. They are the "building blocks" of the hadrons. They are also the only particles to be affected by the strong interaction.
  
  The leptons had been detected since 1897, when J. J. Thomson had shown that electric current is a flow of electrons. Some bosons were being routinely detected, although the W, W and Z particles of the electroweak force were only categorically seen in the early 1980s, and gluons were only firmly pinned down at DESY in Hamburg at about the same time. Quarks, however, were still elusive.
   Given the above, the primary method for imaging particle analysis is using optical microscopy. While optical microscopes have been around and used for particle analysis since the 1600s, the "analysis" in the past has been accomplished by humans using the human visual system. As such, much of this analysis is subjective, or qualitative in nature. Even when some sort of qualitative tools are available, such as a measuring reticle in the microscope, it has still required a human to determine and record those measurements.
   BULLET::::- The up quark is a first-generation quark with a charge of +(2/3)e. The existence of up quarks was first postulated when Murray Gell-Mann and George Zweig developed the quark model in 1964, and the first evidence for them was found in deep inelastic scattering experiments in 1968.
  
  1968 Down quark
   The tight cone of particles created by the hadronization of a single quark is called a jet. In particle detectors, jets are observed rather than quarks, whose existence must be inferred. The models and approximation schemes and their predicted jet hadronization, or fragmentation, have been extensively compared with measurement in a number of high energy particle physics experiments, e.g. TASSO, OPAL and H1.
  
  Hadronization also occurred shortly after the Big Bang when the quark–gluon plasma cooled to the temperature below which free quarks and gluons cannot exist (about 170 MeV). The quarks and gluons then combined into hadrons.
   As faster computing resources became available at lowered costs, the task of making measurements from microscope images of particles could now be performed automatically by machine without human intervention, making it possible to measure significantly larger numbers of particles in much less time.
  
  Section::::Image acquisition methods.
  
  The basic process by which imaging particle analysis is carried out is as follows:
  
  BULLET::::1. A digital camera captures an image of the field of view in the optical system.
   In 1947, the first true mesons, the charged pions, were found by the collaboration of Cecil Powell, César Lattes, Giuseppe Occhialini, "et al.", at the University of Bristol, in England. Since the advent of particle accelerators had not yet come, high-energy subatomic particles were only obtainable from atmospheric cosmic rays. Photographic emulsions based on the gelatin-silver process were placed for long periods of time in sites located at high altitude mountains, first at Pic du Midi de Bigorre in the Pyrenees, and later at Chacaltaya in the Andes Mountains, where the plates were struck by cosmic rays.
   Starting in 1969, deep inelastic scattering experiments at SLAC revealed surprising experimental evidence for particles inside of protons. Whether these were quarks or something else was not known at first. Many experiments were needed to fully identify the properties of the subprotonic components. To a first approximation, they were indeed the already-described quarks.
   Section::::Electrons.
  
  When an electron is the incident particle, the probability of inelastic scattering, depending on the energy of the incident electron, is usually smaller than that of elastic scattering. Thus in the case of gas electron diffraction, reflection high-energy electron diffraction (RHEED), and transmission electron diffraction, because the energy of the incident electron is high, the contribution of inelastic electron scattering can be ignored. Deep inelastic scattering of electrons from protons provided the first direct evidence for the existence of quarks.
  
  Section::::Photons.
   A historic method of secondary particle detection still used for demonstration purposes involves the use of cloud chambers to detect the secondary muons created when a pion decays. Cloud chambers in particular can be built from widely available materials and can be constructed even in a high-school laboratory. A fifth method, involving bubble chambers, can be used to detect cosmic ray particles.
   BULLET::::- D mesons are the lightest particle containing charm quarks. They are often studied to gain knowledge on the weak interaction. Since the D meson is the lightest meson containing a charm quark, it must change the charm quark into another quark to decay. D mesons were discovered in 1976 during the Mark I experiments at the Stanford Linear Accelerator Center.
  
  1976 Hepatitis B virus vaccine
  
  BULLET::::- After Baruch Samuel Blumberg discovered the Hepatitis B virus in 1964, he later developed a diagnostic test and vaccine for the Hepatitis B virus in 1976.
  
  1977 Tau lepton
   ALICE recorded data from the first lead-lead collisions at the LHC in 2010. Data sets taken during heavy-ion periods in 2010 and 2011 as well as proton-lead data from 2013 have provided an excellent basis for an in-depth look at the physics of quark–gluon plasma.
  
  Section::::Heavy-ion collisions at the LHC.
   Finally, beginning roughly in the late 1970s, CCD digital sensors for capturing images and computers which could process those images, began to revolutionize the process by using digital imaging. Although the actual algorithms for performing digital image processing had been around for some time, it was not until the significant computing power needed to perform these analyses became available at reasonable prices that digital imaging techniques could be brought to bear in the mainstream. The first dynamic imaging particle analysis system was patented in 1982.
   BULLET::::- The upsilon meson is a flavorless meson formed from a bottom quark and its antiparticle. It was discovered by the E288 collaboration, headed by Leon Lederman, at Fermilab in 1977, and was the first particle containing a bottom quark to be discovered because it is the lightest that can be produced without additional massive particles. It has a mean lifetime of 1.21×10 second and a mass about 10 GeV.
  
  1977 Bottom quark
   Often data sets of tens of thousands of particle images are used, and to reach an optimal solution an iterative procedure of alignment and classification is used, whereby strong image averages produced by classification are used as reference images for a subsequent alignment of the whole data set.
  
  Section::::Techniques.:Image filtering.
   BULLET::::- 1977 to 1995 – The top quark is finally observed by a team at Fermilab after an 18-year search. It has a mass much greater than had been previously expected — almost as great as a gold atom.
   The technique was not developed further until the 1970s, when Albert Crewe at the University of Chicago developed the field emission gun and added a high quality objective lens to create a modern STEM. He demonstrated the ability to image atoms using an annular dark field detector. Crewe and coworkers at the University of Chicago developed the cold field emission electron source and built a STEM able to visualize single heavy atoms on thin carbon substrates.
   BULLET::::- The charm quark is a second-generation quark with an electric charge of +2⁄3 e. It is the third most massive of the quarks, at about 1.5 GeV/c2 and roughly one and a half times the mass of the proton. It was predicted in 1964 by Sheldon Lee Glashow and James Bjorken and first observed in November 1974, with the simultaneous discovery of the J/ψ|J/ψ meson charm particle at Stanford Linear Accererator Center by a group led by Burton Richter and at Brookhaven National Laboratory by a group led by Samuel C. C. Ting.
  
  1974 Binary pulsars
   BULLET::::- 1974 – Burton Richter and Samuel Ting: Charm quarks are produced almost simultaneously by two teams in November 1974 (see November Revolution) — one at SLAC under Burton Richter, and one at Brookhaven National Laboratory under Samuel Ting. The charm quarks are observed bound with charm antiquarks in mesons. The two discovering parties independently assign the discovered meson two different symbols, J and ψ; thus, it becomes formally known as the J/ψ meson. The discovery finally convinces the physics community of the quark model's validity.
   BULLET::::- The bottom quark is a third-generation quark with a charge of −1⁄3e. The bottom quark was discovered by the E288 experiment at Fermilab in 1977 when collisions produced bottomonium.
  
  1978 Restriction endonucleases
   BULLET::::4. The measurements saved for each particle are then used to generate image population statistics, or as inputs to algorithms for filtering and sorting the particles into groups of similar types. In some systems, sophisticated pattern recognition techniques may also be employed in order to separate different particle types contained in a heterogeneous sample.
  
  Imaging particle analyzers can be subdivided into two distinct types, static and dynamic, based upon the image acquisition methods. While the basic principles are the same, the methods of image acquisition are different in nature, and each has advantages and disadvantages.
   Section::::The physics of STAR.
  
  In the immediate aftermath of the Big Bang, the expanding matter was so hot and dense that protons and neutrons could not exist. Instead, the early universe comprised a plasma of quarks and gluons, which in today's cool universe are confined and exist only within composite particles (bound states) – the hadrons, such as protons and neutrons. Collisions of heavy nuclei at sufficiently high energies allow physicists to study whether quarks and gluons become deconfined at high densities, and if so, what the properties of this matter (i.e. quark–gluon plasma) are.
   Murray Gell-Mann along with George Zweig first proposed fractionally charged quarks in 1961. Throughout the 1960s, different authors considered theories similar to the modern fundamental theory of quantum chromodynamics (QCD) as simple models for the interactions of quarks. The first to hypothesize the gluons of QCD were Moo-Young Han and Yoichiro Nambu, who introduced the quark color charge and hypothesized that it might be associated with a force-carrying field. At that time, however, it was difficult to see how such a model could permanently confine quarks. Han and Nambu also assigned each quark color an integer electrical charge, so that the quarks were fractionally charged only on average, and they did not expect the quarks in their model to be permanently confined.
   BULLET::::2. A gray scale thresholding process is used to perform image segmentation, segregating out the particles from the background, creating a binary image of each particle.
  
  BULLET::::3. Digital image processing techniques are used to perform image analysis operations, resulting in morphological and grey-scale measurements to be stored for each particle.
   The sample is prepared on a microscope slide which is placed on the microscope stage. Once the sample has been focused on, then an image can be acquired and displayed on the monitor. If it is a digital camera or a frame grabber is present, the image can now be saved in digital format, and image processing algorithms can be used to isolate particles in the field of view and measure them.
  
presuppositions: Because atoms are incredibly small and can't be seen by the eye, quarks shouldn't of been able to be discovered due to their size.
corrections: Although quarks were never seen, they were discovered by the math and not by sight.
raw_presuppositions: Because atoms are incredibly small and can't be seen by the eye, quarks shouldn't of been able to be discovered due to their size. We can see quarks.
raw_corrections: Although quarks were never seen, they were discovered by the math and not by sight. We can't see quarks we just say they exist because they solve the math and physics. If another theory without them could solve the math and physics then they would not exist. 