The ImageJ ecosystem: An open platform for biomedical image analysis

Molecular Reproduction and Development

Volumn 82, Issue 7-8, 2015, Pages 518-529

  Schindelin, Johannes ^a   Rueden, Curtis T ^a   Hiner, Mark C ^a   Eliceiri, Kevin W ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOMEDICINE; CASE STUDY; IMAGE ACQUISITION; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE REGISTRATION; IMAGE SEGMENTATION; IMAGE TRACKING; IMAGING SOFTWARE; PRIORITY JOURNAL; REVIEW; DEVICES; FLUORESCENCE IMAGING; HUMAN; MICROSCOPY; PROCEDURES; SOFTWARE;

HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY; OPTICAL IMAGING; SOFTWARE;

EID: 84937729004     PISSN: 1040452X     EISSN: 10982795     Source Type: Journal    
DOI: 10.1002/mrd.22489     Document Type: Review

References (40)

1. Allan C, Burel J, Moore J, Blackburn C, Linkert M, Loynton S, MacDonald D, Moore WJ, Neves C, Patterson A, Porter M, Tarkowska A, Loranger B, Avondo J, Lagerstedt I, Lianas L, Leo S, Hands K, Hay RT, Patwardhan A, Best C, Kleywegt GJ, Zanetti G, Swedlow JR. 2012. OMERO: Flexible, model-driven data management for experimental biology. Nat Methods 9:245-253.
2. Arganda-Carreras I. 2008. bUnwarpj: Consistent and elastic registration in imagej, methods and applications. Second ImageJ User & Developer Conference.
3. Austenfeld M, Beyschlag W. 2012. A Graphical User Interface for R in a Rich Client Platform for Ecological Modeling. J Stat Software 49:1-19.
4. Benmansour F, Longair M, Turetken E, Schindelin J, Fua P. 2012. Bioimage Analysis Workshop, 2012. Spain: Barcelona.
5. Berthold MR, Cebron N, Dill F, Gabriel TR, Kötter T, Meinl T, Ohl P, Sieb C, Thiel K, Wiswedel B. 2008. KNIME: The Konstanz information miner. Data Analysis, Machine Learning and Applications 319-326.
6. Bradski G. 2000. The OpenCV library. Doctor Dobbs J 25:120-126.
7. Burger W, Burge MJ. 2010. Principles of Digital Image Processing. New York: Springer. p 1-221.
8. Cardona A, Saalfeld S, Schindelin J, Arganda-Carreras I, Preibisch S, Longair M, Tomancak P, Hartenstein V, Douglas RJ. 2012. TrakEM2 software for neural circuit reconstruction. PLoS ONE 7:e38011.
9. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM. 2006. CellProfiler: Image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7:R100.
10. Castleman K. 1996. Digital Image Processing. Upper Saddle River 1-667.
11. de Chaumont F, Dallongeville S, Chenouard N, Hervé N, Pop S, Provoost T, Meas-Yedid V, Pankajakshan P, Lecomte T, Montagner YL, Lagache T, Dufour A, Olivo-Marin J. 2012. Icy: An open bioimage informatics platform for extended reproducible research. Nat Methods 9:690-696.
12. Collins TJ. 2007. ImageJ for microscopy. BioTechn 43:25-30.
13. Cristy J, Bergougnoux K, Bogart R, Peterson JW, Brown N, Chiarappa M, Crimmins TR, Zimmermann A. 1994. ImageMagick. Currently available at http://ftp.x.org/contrib/applications/ImageMagick/ImageMagick-3.0.tar.gz.
14. Delgado-Gonzalo R, Thevenaz P, Seelamantula CS, Unser M. 2012. Snakes with an ellipse-reproducing property. Image Process, IEEE Trans On 21:1258-1271.
15. Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Swedlow J, Tomancak P, Carpenter AE. 2012. Biological imaging software tools. Nat Methods 9:697-710.
16. Forster B, Van De Ville D, Berent J, Sage D, Unser M. 2004. Complex wavelets for extended depth-of-field: A new method for the fusion of multichannel microscopy images. Microsc Res Tech 65:33-42.
17. Hegge S, Kudryashev M, Smith A, Frischknecht F. 2009. Automated classification of Plasmodium sporozoite movement patterns reveals a shift towards productive motility during salivary gland infection. Biotechnol J 4:903-913.
18. Henriksson J, Hench J, Tong YG, Johansson A, Johansson D, Bürglin TR. 2013. Endrov: An integrated platform for image analysis. Nat Methods 10:454-456.
19. Hibbard B. 1998. VisAD: Connecting people to computations and people to people. ACM SIGGRAPH Comput Graphics 32:10-12.
20. Inoue S. 1981. Video image processing greatly enhances contrast, quality, and speed in polarization-based microscopy. Journal Cell Biol 89:346-356.
21. Kaynig V, Fuchs T, Buhmann JM. 2010. Neuron geometry extraction by perceptual grouping in sstem images. In Computer Vision and Pattern Recognition (CVPR), June 2010 IEEE Conference on 2902-2909.
22. Konstantinides K, Rasure JR. 1994. The Khoros software development environment for image and signal processing. Image Processing. IEEE Trans On 3:243-252.
23. Köthe U. 2000. Generische Programmierung für die Bildverarbeitung. Dissertation, Fachbereich Informatik. Universität Hamburg, ISBN. 3-8311-0239-2.
24. Linkert M, Rueden CT, Allan C, Burel JM, Moore W, Patterson A, Loranger B, Moore J, Neves C, MacDonald D, Tarkowska A, Sticco C, Hill E, Rossner M, Eliceiri K, Swedlow JR. 2010. Metadata matters: Access to image data in the real world. J Cell biol 189:777-782.
25. Long F, Zhou J, Peng H. 2012. Visualization and analysis of 3D microscopic images. PLoS Comput Biol 8:e1002519.
26. Longair MH, Baker DA, Armstrong JD. 2011. Simple Neurite Tracer: Open Source software for reconstruction, visualization and analysis of neuronal processes. Bioinformatics 27:2453-2454.
27. Meijering E, Smal I, Danuser G. 2006. Tracking in molecular bioimaging. Signal Process Mag IEEE 23:46-53.
28. Möller B, Greß O, Posch S. 2011. Knowing what happened-automatic documentation of image analysis processes. Computer Vision Systems. Berlin Heidelberg: Springer. p 1-10.
29. Pham DL, Xu C, Prince JL. 2000. Current methods in medical image segmentation. Annu Rev Biomed Eng 2:315-337.
30. Pietzsch T, Preibisch S, Tomančák P, Saalfeld S. 2012. ImgLib2-generic image processing in Java. Bioinformatics 28:3009-3011.
31. Pitrone P, Schindelin J, Stuyvenberg L, Preibisch S, Weber M, Eliceiri KW, Huisken J, Tomancak P. 2013. OpenSPIM-an open access platform for light sheet microscopy. Nat Methods 10:598-599.
32. Preibisch S, Saalfeld S, Tomancak P. 2009. Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics 25:1463-1465.
33. Sacha JP, Cockman MD, Dufresne TE, Trokhan D. 2003. Quantification of regional fat volume in rat MRI. Med Imaging 2003:289-297.
34. Sage D, Prodanov D, Tinevez JY, Schindelin J. 2012. MIJ: Making Interoperability Between ImageJ and Matlab Possible. ImageJ User & Developer Conference, 24-26 October 2012, Luxembourg.
35. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez J, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. 2012. Fiji: An open-source platform for biological-image analysis. Nat Methods 9:676-682.
36. Schmid B, Schindelin J, Cardona A, Longair M, Heisenberg M. 2010. A high-level 3D visualization API for Java and ImageJ. BMC Bioinf 11:274.
37. Schneider CA, Rasband WS, Eliceiri KW. 2012. NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9:671-675.
38. Sluder G, Wolf D. 2007. Digital Microscopy, volume 81 (Methods in Cell Biology). Acad Press. 1-632.
39. Stuurman N, Amdodaj N, Vale R. 2007. Micro-Manager: Open Source software for light microscope imaging. Microsc Today 15:42-43.
40. Yoo TS, Ackerman MJ, Lorensen WE, Schroeder W, Chalana V, Aylward S, Metaxas D, Whitaker R. 2002. Engineering and algorithm design for an image processing api: A technical report on itk-the insight toolkit. Stud Health Technol Inf 586-592.