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Literature DB >> 22743769

Why bioimage informatics matters.

Abstract

Driven by the importance of spatial and physical factors in cellular processes and the size and complexity of modern image data, computational analysis of biological imagery has become a vital emerging sub-discipline of bioinformatics and computer vision.

Mesh：

Year: 2012 PMID： 22743769 DOI： 10.1038/nmeth.2024

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

13 in total

1. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.

Authors: Richard J Mural; Mark D Adams; Eugene W Myers; Hamilton O Smith; George L Gabor Miklos; Ron Wides; Aaron Halpern; Peter W Li; Granger G Sutton; Joe Nadeau; Steven L Salzberg; Robert A Holt; Chinnappa D Kodira; Fu Lu; Lin Chen; Zuoming Deng; Carlos C Evangelista; Weiniu Gan; Thomas J Heiman; Jiayin Li; Zhenya Li; Gennady V Merkulov; Natalia V Milshina; Ashwinikumar K Naik; Rong Qi; Bixiong Chris Shue; Aihui Wang; Jian Wang; Xin Wang; Xianghe Yan; Jane Ye; Shibu Yooseph; Qi Zhao; Liansheng Zheng; Shiaoping C Zhu; Kendra Biddick; Randall Bolanos; Arthur L Delcher; Ian M Dew; Daniel Fasulo; Michael J Flanigan; Daniel H Huson; Saul A Kravitz; Jason R Miller; Clark M Mobarry; Knut Reinert; Karin A Remington; Qing Zhang; Xiangqun H Zheng; Deborah R Nusskern; Zhongwu Lai; Yiding Lei; Wenyan Zhong; Alison Yao; Ping Guan; Rui-Ru Ji; Zhiping Gu; Zhen-Yuan Wang; Fei Zhong; Chunlin Xiao; Chia-Chien Chiang; Mark Yandell; Jennifer R Wortman; Peter G Amanatides; Suzanne L Hladun; Eric C Pratts; Jeffery E Johnson; Kristina L Dodson; Kerry J Woodford; Cheryl A Evans; Barry Gropman; Douglas B Rusch; Eli Venter; Mei Wang; Thomas J Smith; Jarrett T Houck; Donald E Tompkins; Charles Haynes; Debbie Jacob; Soo H Chin; David R Allen; Carl E Dahlke; Robert Sanders; Kelvin Li; Xiangjun Liu; Alexander A Levitsky; William H Majoros; Quan Chen; Ashley C Xia; John R Lopez; Michael T Donnelly; Matthew H Newman; Anna Glodek; Cheryl L Kraft; Marc Nodell; Feroze Ali; Hui-Jin An; Danita Baldwin-Pitts; Karen Y Beeson; Shuang Cai; Mark Carnes; Amy Carver; Parris M Caulk; Angela Center; Yen-Hui Chen; Ming-Lai Cheng; My D Coyne; Michelle Crowder; Steven Danaher; Lionel B Davenport; Raymond Desilets; Susanne M Dietz; Lisa Doup; Patrick Dullaghan; Steven Ferriera; Carl R Fosler; Harold C Gire; Andres Gluecksmann; Jeannine D Gocayne; Jonathan Gray; Brit Hart; Jason Haynes; Jeffery Hoover; Tim Howland; Chinyere Ibegwam; Mena Jalali; David Johns; Leslie Kline; Daniel S Ma; Steven MacCawley; Anand Magoon; Felecia Mann; David May; Tina C McIntosh; Somil Mehta; Linda Moy; Mee C Moy; Brian J Murphy; Sean D Murphy; Keith A Nelson; Zubeda Nuri; Kimberly A Parker; Alexandre C Prudhomme; Vinita N Puri; Hina Qureshi; John C Raley; Matthew S Reardon; Megan A Regier; Yu-Hui C Rogers; Deanna L Romblad; Jakob Schutz; John L Scott; Richard Scott; Cynthia D Sitter; Michella Smallwood; Arlan C Sprague; Erin Stewart; Renee V Strong; Ellen Suh; Karena Sylvester; Reginald Thomas; Ni Ni Tint; Christopher Tsonis; Gary Wang; George Wang; Monica S Williams; Sherita M Williams; Sandra M Windsor; Keriellen Wolfe; Mitchell M Wu; Jayshree Zaveri; Kabir Chaturvedi; Andrei E Gabrielian; Zhaoxi Ke; Jingtao Sun; Gangadharan Subramanian; J Craig Venter; Cynthia M Pfannkoch; Mary Barnstead; Lisa D Stephenson
Journal: Science Date: 2002-05-31 Impact factor: 47.728

2. Polarization of PAR proteins by advective triggering of a pattern-forming system.

Authors: Nathan W Goehring; Philipp Khuc Trong; Justin S Bois; Debanjan Chowdhury; Ernesto M Nicola; Anthony A Hyman; Stephan W Grill
Journal: Science Date: 2011-10-20 Impact factor: 47.728

3. Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development.

Authors: Philipp J Keller; Annette D Schmidt; Jochen Wittbrodt; Ernst H K Stelzer
Journal: Cold Spring Harb Protoc Date: 2011-10-01

4. BioImageXD: an open, general-purpose and high-throughput image-processing platform.

Authors: Pasi Kankaanpää; Lassi Paavolainen; Silja Tiitta; Mikko Karjalainen; Joacim Päivärinne; Jonna Nieminen; Varpu Marjomäki; Jyrki Heino; Daniel J White
Journal: Nat Methods Date: 2012-06-28 Impact factor: 28.547

5. Fiji: an open-source platform for biological-image analysis.

Authors: Johannes Schindelin; Ignacio Arganda-Carreras; Erwin Frise; Verena Kaynig; Mark Longair; Tobias Pietzsch; Stephan Preibisch; Curtis Rueden; Stephan Saalfeld; Benjamin Schmid; Jean-Yves Tinevez; Daniel James White; Volker Hartenstein; Kevin Eliceiri; Pavel Tomancak; Albert Cardona
Journal: Nat Methods Date: 2012-06-28 Impact factor: 28.547

6. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans.

Authors: B Sönnichsen; L B Koski; A Walsh; P Marschall; B Neumann; M Brehm; A-M Alleaume; J Artelt; P Bettencourt; E Cassin; M Hewitson; C Holz; M Khan; S Lazik; C Martin; B Nitzsche; M Ruer; J Stamford; M Winzi; R Heinkel; M Röder; J Finell; H Häntsch; S J M Jones; M Jones; F Piano; K C Gunsalus; K Oegema; P Gönczy; A Coulson; A A Hyman; C J Echeverri
Journal: Nature Date: 2005-03-24 Impact factor: 49.962

7. Global analysis of protein expression in yeast.

Authors: Sina Ghaemmaghami; Won-Ki Huh; Kiowa Bower; Russell W Howson; Archana Belle; Noah Dephoure; Erin K O'Shea; Jonathan S Weissman
Journal: Nature Date: 2003-10-16 Impact factor: 49.962

Review 8. Genome sequence of the nematode C. elegans: a platform for investigating biology.

Authors:
Journal: Science Date: 1998-12-11 Impact factor: 47.728

9. The sequence of the human genome.

Authors: J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal: Science Date: 2001-02-16 Impact factor: 47.728

10. The genome sequence of Drosophila melanogaster.

Authors: M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter
Journal: Science Date: 2000-03-24 Impact factor: 47.728

20 in total

1. Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains.

Authors: Shengdian Jiang; Yimin Wang; Lijuan Liu; Liya Ding; Zongcai Ruan; Hong-Wei Dong; Giorgio A Ascoli; Michael Hawrylycz; Hongkui Zeng; Hanchuan Peng
Journal: Neuroinformatics Date: 2022-02-19

2. A bioimage informatics based reconstruction of breast tumor microvasculature with computational blood flow predictions.

Authors: Spyros K Stamatelos; Eugene Kim; Arvind P Pathak; Aleksander S Popel
Journal: Microvasc Res Date: 2013-12-14 Impact factor: 3.514

Why bioimage informatics matters.

1. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.

2. Polarization of PAR proteins by advective triggering of a pattern-forming system.

3. Digital scanned laser light-sheet fluorescence microscopy (DSLM) of zebrafish and Drosophila embryonic development.

4. BioImageXD: an open, general-purpose and high-throughput image-processing platform.

5. Fiji: an open-source platform for biological-image analysis.

6. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans.

7. Global analysis of protein expression in yeast.

Review 8. Genome sequence of the nematode C. elegans: a platform for investigating biology.

9. The sequence of the human genome.

10. The genome sequence of Drosophila melanogaster.

1. Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains.

2. A bioimage informatics based reconstruction of breast tumor microvasculature with computational blood flow predictions.

3. Statistical comparison of spatial point patterns in biological imaging.

4. Automated quantification of aligned collagen for human breast carcinoma prognosis.

5. Open source software for quantification of cell migration, protrusions, and fluorescence intensities.

6. Collaborative analysis of multi-gigapixel imaging data using Cytomine.

7. CalloseMeasurer: a novel software solution to measure callose deposition and recognise spreading callose patterns.

8. Light microscopy applications in systems biology: opportunities and challenges.

9. An imaging-based platform for high-content, quantitative evaluation of therapeutic response in 3D tumour models.

10. Image Quality Ranking Method for Microscopy.