DOI: 10.1016/j.jsb.2009.01.004. DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy

DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy

10.1016/j.jsb.2009.01.004

Crossref journal-article

Elsevier BV

Journal of Structural Biology (78)

Bibliography

Voss, N. R., Yoshioka, C. K., Radermacher, M., Potter, C. S., & Carragher, B. (2009). DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy. Journal of Structural Biology, 166(2), 205â213.

Authors 5

N.R. Voss (first)
C.K. Yoshioka (additional)
M. Radermacher (additional)
C.S. Potter (additional)
B. Carragher (additional)

References 27 Referenced 575

10.1016/j.jsb.2005.09.007 / J. Struct. Biol. / Particle picking by segmentation: a comparative study with SPIDER-based manual particle picking by Adiga (2005)
10.1016/j.jsb.2006.06.001 / J. Struct. Biol. / SIGNATURE: a single-particle selection system for molecular electron microscopy by Chen (2007)
10.1113/jphysiol.1966.sp008107 / J. Physiol. / The contrast sensitivity of retinal ganglion cells of the cat by Enroth-Cugell (1966)
10.1006/jsbi.1996.0030 / J. Struct. Biol. / SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields by Frank (1996)
10.1109/JPROC.2004.840301 / Proc. IEEE / The design and implementation of FFTW3 by Frigo (2005)
10.1016/j.jsb.2003.09.005 / J. Struct. Biol. / Historical background: why is it important to improve automated particle selection methods? by Glaeser (2004)
10.1017/S003358350000305X / Q. Rev. Biophys. / The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules by Henderson (1995)
Jones, E., Oliphant, T., et al., 2001. SciPy: Open Source Scientific Tools for Python
10.1016/j.jsb.2005.10.012 / J. Struct. Biol. / The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles by Leschziner (2006)
{'issue': '21', 'key': '10.1016/j.jsb.2009.01.004_bib10', 'first-page': '2', 'article-title': 'Scale-space theory: a basic tool for analysing structures at different scales', 'author': 'Lindeberg', 'year': '1994', 'journal-title': 'J. Appl. Stat.'} / J. Appl. Stat. / Scale-space theory: a basic tool for analysing structures at different scales by Lindeberg (1994)
10.1016/j.jsb.2003.11.005 / J. Struct. Biol. / Detecting particles in cryo-EM micrographs using learned features by Mallick (2004)
10.1371/journal.pbio.0050209 / PLoS Biol. / Structure of the chloroplast ribosome: novel domains for translation regulation by Manuell (2007)
10.1523/JNEUROSCI.5252-03.2004 / J. Neurosci. / The classical receptive field surround of primate parasol ganglion cells is mediated primarily by a non-GABAergic pathway by McMahon (2004)
Radermacher, M., Wagenknecht, T., et al., 1986. A new 3-D reconstruction scheme applied to the 50S ribosomal subunit of E. coli. J. Microsc. 141 (Pt. 1), RP1–RP2. (10.1111/j.1365-2818.1986.tb02693.x)
10.1016/j.jsb.2003.11.007 / J. Struct. Biol. / FindEM—a fast, efficient program for automatic selection of particles from electron micrographs by Roseman (2004)
10.1016/j.jsb.2006.08.003 / J. Struct. Biol. / Ab initio resolution measurement for single particle structures by Sousa (2007)
10.1016/j.jsb.2008.04.005 / J. Struct. Biol. / A test-bed for optimizing high-resolution single particle reconstructions by Stagg (2008)
10.1016/j.jsb.2005.03.010 / J. Struct. Biol. / Automated molecular microscopy: the new Leginon system by Suloway (2005)
10.1016/j.jmb.2004.12.031 / J. Mol. Biol. / Refined structure of the nicotinic acetylcholine receptor at 4 Å resolution by Unwin (2005)
10.1016/j.jmb.2003.12.015 / J. Mol. Biol. / Recognition and separation of single particles with size variation by statistical analysis of their images by White (2004)
10.1016/j.jsb.2007.03.003 / J. Struct. Biol. / The Laplacian of Gaussian and arbitrary z-crossings approach applied to automated single particle reconstruction by Woolford (2007)
10.1016/j.jsb.2007.03.005 / J. Struct. Biol. / Automation of random conical tilt and orthogonal tilt data collection using feature-based correlation by Yoshioka (2007)
10.1163/156856887X00222 / Spat. Vis. / The Gaussian derivative model for spatial vision: I. Retinal mechanisms by Young (1987)
10.1038/nature06893 / Nature / 3.88Å structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy by Yu (2008)
10.1073/pnas.0711623105 / Proc. Natl. Acad. Sci. USA / Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction by Zhang (2008)
10.1016/j.jsb.2003.09.033 / J. Struct. Biol. / Automatic particle selection: results of a comparative study by Zhu (2004)
10.1109/TMI.2003.816947 / IEEE Trans. Med. Imaging / Automatic particle detection through efficient Hough transforms by Zhu (2003)

Dates

Type	When
Created	16 years, 7 months ago (Jan. 19, 2009, 11:12 p.m.)
Deposited	6 years, 7 months ago (Dec. 22, 2018, 2:28 a.m.)
Indexed	22 hours, 23 minutes ago (Aug. 20, 2025, 8:42 a.m.)
Issued	16 years, 3 months ago (May 1, 2009)
Published	16 years, 3 months ago (May 1, 2009)
Published Print	16 years, 3 months ago (May 1, 2009)

Funders 0

None

BibTeX

@article{Voss_2009, title={DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy}, volume={166}, ISSN={1047-8477}, url={http://dx.doi.org/10.1016/j.jsb.2009.01.004}, DOI={10.1016/j.jsb.2009.01.004}, number={2}, journal={Journal of Structural Biology}, publisher={Elsevier BV}, author={Voss, N.R. and Yoshioka, C.K. and Radermacher, M. and Potter, C.S. and Carragher, B.}, year={2009}, month=may, pages={205–213} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        8,
        20
      ]
    ],
    "date-time": "2025-08-20T12:42:51Z",
    "timestamp": 1755693771085
  },
  "reference-count": 27,
  "publisher": "Elsevier BV",
  "issue": "2",
  "license": [
    {
      "start": {
        "date-parts": [
          [
            2009,
            5,
            1
          ]
        ],
        "date-time": "2009-05-01T00:00:00Z",
        "timestamp": 1241136000000
      },
      "content-version": "tdm",
      "delay-in-days": 0,
      "URL": "https://www.elsevier.com/tdm/userlicense/1.0/"
    }
  ],
  "content-domain": {
    "domain": [],
    "crossmark-restriction": false
  },
  "published-print": {
    "date-parts": [
      [
        2009,
        5
      ]
    ]
  },
  "DOI": "10.1016/j.jsb.2009.01.004",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2009,
        1,
        20
      ]
    ],
    "date-time": "2009-01-20T04:12:35Z",
    "timestamp": 1232424755000
  },
  "page": "205-213",
  "source": "Crossref",
  "is-referenced-by-count": 575,
  "title": "DoG Picker and TiltPicker: Software tools to facilitate particle selection in single particle electron microscopy",
  "prefix": "10.1016",
  "volume": "166",
  "author": [
    {
      "given": "N.R.",
      "family": "Voss",
      "sequence": "first",
      "affiliation": []
    },
    {
      "given": "C.K.",
      "family": "Yoshioka",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "M.",
      "family": "Radermacher",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "C.S.",
      "family": "Potter",
      "sequence": "additional",
      "affiliation": []
    },
    {
      "given": "B.",
      "family": "Carragher",
      "sequence": "additional",
      "affiliation": []
    }
  ],
  "member": "78",
  "reference": [
    {
      "issue": "3",
      "key": "10.1016/j.jsb.2009.01.004_bib1",
      "doi-asserted-by": "crossref",
      "first-page": "211",
      "DOI": "10.1016/j.jsb.2005.09.007",
      "article-title": "Particle picking by segmentation: a comparative study with SPIDER-based manual particle picking",
      "volume": "152",
      "author": "Adiga",
      "year": "2005",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "1",
      "key": "10.1016/j.jsb.2009.01.004_bib2",
      "doi-asserted-by": "crossref",
      "first-page": "168",
      "DOI": "10.1016/j.jsb.2006.06.001",
      "article-title": "SIGNATURE: a single-particle selection system for molecular electron microscopy",
      "volume": "157",
      "author": "Chen",
      "year": "2007",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "3",
      "key": "10.1016/j.jsb.2009.01.004_bib3",
      "doi-asserted-by": "crossref",
      "first-page": "517",
      "DOI": "10.1113/jphysiol.1966.sp008107",
      "article-title": "The contrast sensitivity of retinal ganglion cells of the cat",
      "volume": "187",
      "author": "Enroth-Cugell",
      "year": "1966",
      "journal-title": "J. Physiol."
    },
    {
      "issue": "1",
      "key": "10.1016/j.jsb.2009.01.004_bib4",
      "doi-asserted-by": "crossref",
      "first-page": "190",
      "DOI": "10.1006/jsbi.1996.0030",
      "article-title": "SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields",
      "volume": "116",
      "author": "Frank",
      "year": "1996",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "2",
      "key": "10.1016/j.jsb.2009.01.004_bib5",
      "doi-asserted-by": "crossref",
      "first-page": "216",
      "DOI": "10.1109/JPROC.2004.840301",
      "article-title": "The design and implementation of FFTW3",
      "volume": "93",
      "author": "Frigo",
      "year": "2005",
      "journal-title": "Proc. IEEE"
    },
    {
      "issue": "1\u20132",
      "key": "10.1016/j.jsb.2009.01.004_bib6",
      "doi-asserted-by": "crossref",
      "first-page": "15",
      "DOI": "10.1016/j.jsb.2003.09.005",
      "article-title": "Historical background: why is it important to improve automated particle selection methods?",
      "volume": "145",
      "author": "Glaeser",
      "year": "2004",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "2",
      "key": "10.1016/j.jsb.2009.01.004_bib7",
      "doi-asserted-by": "crossref",
      "first-page": "171",
      "DOI": "10.1017/S003358350000305X",
      "article-title": "The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules",
      "volume": "28",
      "author": "Henderson",
      "year": "1995",
      "journal-title": "Q. Rev. Biophys."
    },
    {
      "key": "10.1016/j.jsb.2009.01.004_bib8",
      "unstructured": "Jones, E., Oliphant, T., et al., 2001. SciPy: Open Source Scientific Tools for Python"
    },
    {
      "issue": "3",
      "key": "10.1016/j.jsb.2009.01.004_bib9",
      "doi-asserted-by": "crossref",
      "first-page": "284",
      "DOI": "10.1016/j.jsb.2005.10.012",
      "article-title": "The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles",
      "volume": "153",
      "author": "Leschziner",
      "year": "2006",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "21",
      "key": "10.1016/j.jsb.2009.01.004_bib10",
      "first-page": "2",
      "article-title": "Scale-space theory: a basic tool for analysing structures at different scales",
      "author": "Lindeberg",
      "year": "1994",
      "journal-title": "J. Appl. Stat."
    },
    {
      "issue": "1\u20132",
      "key": "10.1016/j.jsb.2009.01.004_bib11",
      "doi-asserted-by": "crossref",
      "first-page": "52",
      "DOI": "10.1016/j.jsb.2003.11.005",
      "article-title": "Detecting particles in cryo-EM micrographs using learned features",
      "volume": "145",
      "author": "Mallick",
      "year": "2004",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "8",
      "key": "10.1016/j.jsb.2009.01.004_bib12",
      "doi-asserted-by": "crossref",
      "first-page": "e209",
      "DOI": "10.1371/journal.pbio.0050209",
      "article-title": "Structure of the chloroplast ribosome: novel domains for translation regulation",
      "volume": "5",
      "author": "Manuell",
      "year": "2007",
      "journal-title": "PLoS Biol."
    },
    {
      "issue": "15",
      "key": "10.1016/j.jsb.2009.01.004_bib13",
      "doi-asserted-by": "crossref",
      "first-page": "3736",
      "DOI": "10.1523/JNEUROSCI.5252-03.2004",
      "article-title": "The classical receptive field surround of primate parasol ganglion cells is mediated primarily by a non-GABAergic pathway",
      "volume": "24",
      "author": "McMahon",
      "year": "2004",
      "journal-title": "J. Neurosci."
    },
    {
      "key": "10.1016/j.jsb.2009.01.004_bib14",
      "doi-asserted-by": "crossref",
      "unstructured": "Radermacher, M., Wagenknecht, T., et al., 1986. A new 3-D reconstruction scheme applied to the 50S ribosomal subunit of E. coli. J. Microsc. 141 (Pt. 1), RP1\u2013RP2.",
      "DOI": "10.1111/j.1365-2818.1986.tb02693.x"
    },
    {
      "issue": "1\u20132",
      "key": "10.1016/j.jsb.2009.01.004_bib15",
      "doi-asserted-by": "crossref",
      "first-page": "91",
      "DOI": "10.1016/j.jsb.2003.11.007",
      "article-title": "FindEM\u2014a fast, efficient program for automatic selection of particles from electron micrographs",
      "volume": "145",
      "author": "Roseman",
      "year": "2004",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "1",
      "key": "10.1016/j.jsb.2009.01.004_bib16",
      "doi-asserted-by": "crossref",
      "first-page": "201",
      "DOI": "10.1016/j.jsb.2006.08.003",
      "article-title": "Ab initio resolution measurement for single particle structures",
      "volume": "157",
      "author": "Sousa",
      "year": "2007",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "1",
      "key": "10.1016/j.jsb.2009.01.004_bib17",
      "doi-asserted-by": "crossref",
      "first-page": "29",
      "DOI": "10.1016/j.jsb.2008.04.005",
      "article-title": "A test-bed for optimizing high-resolution single particle reconstructions",
      "volume": "163",
      "author": "Stagg",
      "year": "2008",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "1",
      "key": "10.1016/j.jsb.2009.01.004_bib18",
      "doi-asserted-by": "crossref",
      "first-page": "41",
      "DOI": "10.1016/j.jsb.2005.03.010",
      "article-title": "Automated molecular microscopy: the new Leginon system",
      "volume": "151",
      "author": "Suloway",
      "year": "2005",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "4",
      "key": "10.1016/j.jsb.2009.01.004_bib19",
      "doi-asserted-by": "crossref",
      "first-page": "967",
      "DOI": "10.1016/j.jmb.2004.12.031",
      "article-title": "Refined structure of the nicotinic acetylcholine receptor at 4 \u00c5 resolution",
      "volume": "346",
      "author": "Unwin",
      "year": "2005",
      "journal-title": "J. Mol. Biol."
    },
    {
      "issue": "2",
      "key": "10.1016/j.jsb.2009.01.004_bib20",
      "doi-asserted-by": "crossref",
      "first-page": "453",
      "DOI": "10.1016/j.jmb.2003.12.015",
      "article-title": "Recognition and separation of single particles with size variation by statistical analysis of their images",
      "volume": "336",
      "author": "White",
      "year": "2004",
      "journal-title": "J. Mol. Biol."
    },
    {
      "issue": "1",
      "key": "10.1016/j.jsb.2009.01.004_bib21",
      "doi-asserted-by": "crossref",
      "first-page": "122",
      "DOI": "10.1016/j.jsb.2007.03.003",
      "article-title": "The Laplacian of Gaussian and arbitrary z-crossings approach applied to automated single particle reconstruction",
      "volume": "159",
      "author": "Woolford",
      "year": "2007",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "3",
      "key": "10.1016/j.jsb.2009.01.004_bib22",
      "doi-asserted-by": "crossref",
      "first-page": "335",
      "DOI": "10.1016/j.jsb.2007.03.005",
      "article-title": "Automation of random conical tilt and orthogonal tilt data collection using feature-based correlation",
      "volume": "159",
      "author": "Yoshioka",
      "year": "2007",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "4",
      "key": "10.1016/j.jsb.2009.01.004_bib23",
      "doi-asserted-by": "crossref",
      "first-page": "273",
      "DOI": "10.1163/156856887X00222",
      "article-title": "The Gaussian derivative model for spatial vision: I. Retinal mechanisms",
      "volume": "2",
      "author": "Young",
      "year": "1987",
      "journal-title": "Spat. Vis."
    },
    {
      "issue": "7193",
      "key": "10.1016/j.jsb.2009.01.004_bib24",
      "doi-asserted-by": "crossref",
      "first-page": "415",
      "DOI": "10.1038/nature06893",
      "article-title": "3.88\u00c5 structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy",
      "volume": "453",
      "author": "Yu",
      "year": "2008",
      "journal-title": "Nature"
    },
    {
      "issue": "6",
      "key": "10.1016/j.jsb.2009.01.004_bib25",
      "doi-asserted-by": "crossref",
      "first-page": "1867",
      "DOI": "10.1073/pnas.0711623105",
      "article-title": "Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction",
      "volume": "105",
      "author": "Zhang",
      "year": "2008",
      "journal-title": "Proc. Natl. Acad. Sci. USA"
    },
    {
      "issue": "1\u20132",
      "key": "10.1016/j.jsb.2009.01.004_bib26",
      "doi-asserted-by": "crossref",
      "first-page": "3",
      "DOI": "10.1016/j.jsb.2003.09.033",
      "article-title": "Automatic particle selection: results of a comparative study",
      "volume": "145",
      "author": "Zhu",
      "year": "2004",
      "journal-title": "J. Struct. Biol."
    },
    {
      "issue": "9",
      "key": "10.1016/j.jsb.2009.01.004_bib27",
      "doi-asserted-by": "crossref",
      "first-page": "1053",
      "DOI": "10.1109/TMI.2003.816947",
      "article-title": "Automatic particle detection through efficient Hough transforms",
      "volume": "22",
      "author": "Zhu",
      "year": "2003",
      "journal-title": "IEEE Trans. Med. Imaging"
    }
  ],
  "container-title": "Journal of Structural Biology",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://api.elsevier.com/content/article/PII:S1047847709000197?httpAccept=text/xml",
      "content-type": "text/xml",
      "content-version": "vor",
      "intended-application": "text-mining"
    },
    {
      "URL": "https://api.elsevier.com/content/article/PII:S1047847709000197?httpAccept=text/plain",
      "content-type": "text/plain",
      "content-version": "vor",
      "intended-application": "text-mining"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2018,
        12,
        22
      ]
    ],
    "date-time": "2018-12-22T07:28:21Z",
    "timestamp": 1545463701000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://linkinghub.elsevier.com/retrieve/pii/S1047847709000197"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2009,
        5
      ]
    ]
  },
  "references-count": 27,
  "journal-issue": {
    "issue": "2",
    "published-print": {
      "date-parts": [
        [
          2009,
          5
        ]
      ]
    }
  },
  "alternative-id": [
    "S1047847709000197"
  ],
  "URL": "http://dx.doi.org/10.1016/j.jsb.2009.01.004",
  "relation": {},
  "ISSN": [
    "1047-8477"
  ],
  "subject": [],
  "container-title-short": "Journal of Structural Biology",
  "published": {
    "date-parts": [
      [
        2009,
        5
      ]
    ]
  }
}