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Credits

[C1] The ImageJ installer for Windows is created using the Inno Setup installer generator. ImageJ.exethe Windows that launches ImageJ (ij.jar) was contributed by George Silva.

[C2] Support for ZIP-compressed TIFFs was contributed by Jason Newton in IJ 1.45g.

[C3] The Editor↑’s Function Finder (Macros▷Function Finder...) was written by Jérôme Mutterer.

[C4] The Elliptical Selection Tool↑ was contributed by Norbert Vischer.

[C5] The Brush Selection Tool↑ is based on the ROI Brush Toolplugin from Tom Larkworthy and Johannes Schindelin.

[C6] Jean-Yves Tinevez and Johannes Schindelin (authors of the Fiji Arrow Tool) contributed code to the Arrow Tool↑.

[C7] Michael Schmid, added 4--connected and 8--connected tracing with tolerance to the Wand Tool↑.

[C8] Macro Toolsets distributed with ImageJ have been contributed by Gilles Carpentier, Jérôme Mutterer and Tiago Ferreira.

[C9] The Pixel Inspector↑ is a plugin tool conversion of Michael Schmid’s Pixel Inspector plugin.

[C10] In IJ 1.43l and earlier, the File▷Import▷Results…↑ command was based on Jérôme Mutterer’s Import_Results_Table macro.

[C11] Marcel van Herk added URLs support to the File▷Import▷Stack From List…↑ command in IJ 1.45f.

[C12] Michael Schmid contributed improvements to the AVI reader and AVI writer plugins.

[C13] Karen Collins contributed improvements to the FITS_Writer (File▷Save As▷FITS…↑ command).

[C14] The Edit▷Selection▷Fit Circle↑ command, based on a MATLAB script by Nikolai Chernov, was contributed by Michael Doube and Ved Sharma.

[C15] The Edit▷Selection▷Create Selection↑ command is based on the Threshold_To_Selection plugin written by Johannes Schindelin.

[C16] IJ 1.46f adopted Johannes Schindelin’s RMI-based OtherInstance class from Fiji, which works on multi-user machines and is more secure.

[C17] The Color Picker (Image▷Color▷Color Picker… [K]↑) was written by Gali Baler, a 2003--2004 intern from Bethesda-Chevy Chase High School.

[C18] The 16 different thresholding methods available in the Image▷Adjust▷Threshold… [T]↑ tool were implemented by Gabriel Landini.

[C19] Michael Schmid contributed improvements to the downsizing kernel used by Image▷Adjust▷Size…↑ and Image▷Scale… [E]↑ as well as undo support for Image▷Scale… [E]↑ .

[C20] The Image▷Adjust▷Color Threshold…↑ command implements Gabriel Landini’s Threshold Colour plugin.

[C21] The Reslice and the ZProject plugin (Image▷Stacks▷Reslice… [/]↑ and Z Project…↑ commands) were contributed by Patrick Kelly and Harvey Karten of the University of California, San Diego.

[C22] The Image▷Stacks▷Orthogonal Views [H]↑ command is based on Dimiter Prodanov’s StackSlicer plugin and Albert Cardona’s Updater class. Michael Doube added support for XZ and YZ view control as well as mouse wheel control.

[C23] The Image▷Stacks▷3D Project…↑ was written by Michael Castle and Janice Keller of the University of Michigan Mental Health Research Institute (MHRI). Bill Mohler added suport for hyperstacks and 16/32-bit images in IJ 1.44m.

[C24] The Image▷Stacks▷Tools▷Concatenate…↑ command implemented in IJ 1.46e is based on the Concatenate plugin by Jonathan Jackson.

[C25] The Image▷Stacks▷Tools▷Make Substack…↑ command is based on the Substack Makerplugin by Anthony Padua, Daniel Barboriak and Ved Sharma.

[C26] The Image▷Hyperstacks▷Reduce Dimensionality…↑ command is based Jérôme Mutterer’s Reduce HyperStack macro.

[C27] The Image▷Transform▷Bin…↑ command is based on Nico Stuurman’s Binner plugin.

[C28] The Image▷Zoom▷Set…↑ command is based on Albert Cardona’s Zoom Exact plugin.

[C29] The Process▷Find Maxima…↑ command is based on a plugin contributed by Michael Schmid.

[C30] The equalization code implemented in Process▷Enhance Contrast…↑ was contributed by Richard Kirk.

[C31] The Process▷Noise▷Remove NaNs…↑ was contributed by Michael Schmid.

[C32] The Process▷Math▷Macro…↑ command is modeled after Ulf Dittmer’s Expression plugin.

[C33] The Process▷FFT▷Bandpass Filter…↑ is a built in version of Joachim Walter’s FFT Filter plugin.

[C34] The Process▷Binary▷Fill Holes↑ algorithm was contributed by Gabriel Landini.

[C35] The Skeletonize3D plugin was written by Ignacio Arganda-Carreras, based on an ITK[?] implementation by Hanno Homann. It implements a 3D thinning algorithm from Lee et al.  Building skeleton models via 3-D medial surface axis thinning algorithms.  CVGIP, 56(6):462--478, 1994.

[C36] Multi-threading support for all Process▷Filters▷↑ commands was contributed by Stephan Saalfeld and Michael Schmid in ImageJ 1.45c.

[C37] The faster and more accurate version of Process▷Filters▷Gaussian Blur…↑ implemented in ImageJ 1.38r was contributed by Michael Schmid.

[C38] The NonBlockingGenericDialog.class used by the Process▷Batch▷Macro…↑ command was added by Johannes Schindelin.

[C39] The rolling ball code of Process▷Subtract Background…↑ is based on the NIH Image Pascal version by Michael Castle and Janice Keller. The sliding paraboloid algorithm was written by Michael Schmid.

[C40] The Analyze▷Distribution…↑ command was written by Gabriel Landini.

[C41] The scaled color bar implemented in Analyze▷Histogram [h]↑ was contributed by Bob Dougherty.

[C42] The much improved CurveFitter (Analyze▷Tools▷Curve Fitting…↑) implemented in IJ 1.46f was contributed by Michael Schmid. The Rodboard and Gaussian functions were originally contributed by David Rodbard (NIH) and Stefan Wörz (DKFZ), respectively.

[C43] The ROI Manager(XOR) command (Analyze▷Tools▷ROI Manager…↑) was added by Johannes Schindelin.

[C44] The ROI Manager(Multi Measure) command (Analyze▷Tools▷ROI Manager…↑) is based on Bob Dougherty’s Multi_Measure plugin.

[C45] The ROI Manager(Multi Plot) command (Analyze▷Tools▷ROI Manager…↑) was contributed by Philippe Gendre.

[C46] The Analyze▷Tools▷Synchronize Windows↑ command (an improved version of the SyncWindows_ plugin by Patrick Kelly) was contributed by Joachim Walter.

[C47] The Control Panel (Plugins▷Utilities▷Control Panel… [U]↑) was written by Cezar M. Tigare.

[C48] The Command Finder (Plugins▷Utilities▷Find Commands… [l]↑) was written by Mark Longair.

[C49] The PlugInTool class was inspired by Johannes Schindelin’s AbstractTool class in Fiji.

[C50] Other additions, improvements and reproducible bug reports have been contributed by Adrian Daerr, Airen Peraza, Ajay Gopal, Albert Cardona, Alberto Duina, Alden Dima, Andreas Maier, Andrew French, Andrii Savchenko, Arttu Miettinen, Aryeh Weiss, Balazs Nyiri, Barry DeZonia, Bill Mohler, Bob Hamilton, Bob Loushin, Bruno Vellutini, Burri Olivier, Carlos Becker, Carne Draug, Charles Anderson, Cheryl McCreary, Christian Moll, Christophe Leterrier, Christopher Harrison, Damon Poburko, Daniel Hornung, Daniel Kalthoff, Daniel Senff, David Gauntt, David McDonald, Denny Hugg, Dimiter Prodanov, Divakar Ramachandran, Dorai Iyer, Duncan Mak, Eik Schumann, Emmanuel Levy, Erik Meijering, Fabian Svara, Francis Burton, Frank Sprenger, Franklin Shaffer, Frederic Hessman, Gabriel Landini, Gilles Carpentier, Gregory Reneff, Hiroki Hakoshima, Ian Lim, Ingo Bartholomaeus, Jakob Preus, Jamie Robinson, Jan Eglinger, Jan Funke, Jarek Sacha, Jay Unruh, Jean-Pierre Clamme, Jerome Mutterer, Jesper Pedersen, Jim Passmore, Joachim Wesner, Johannes Hermen, Johannes Schindelin, Johannes Weissmann, John Oreopoulos, John Pearl, Jonathan Silver, Jose Wojnacki, Juan Grande, Julian Cooper, Kai Uwe Barthel, Karen Collins, Kees Straatman, Kevin Moll, Kris Sheets, Mark Krebs, Mark Longair, Martin Dressler, Mat Al-Tamimi, Matthew Smith, Michael Cammer, Michael Doube, Michael Ellis, Michael Schmid, Michel Julier, Nagananda Gurudev, Nico Stuurman, Norbert Vischer, Olaf Freyer, Oliver Bannach, Olivier Bardot, Paul Jurczak, Peter Haub, Rainer Engel, Raymond Coory, Reinhard Mayr, Richard Cole, Richie Mort, Robert Dougherty, Shannon Stewman, Simon Roussel, Stefan Starke, Stephan Saalfeld, Steven Green, Thomas Boudier, Thorsten Wagner, Tiago Ferreira, Tomas Karlsson, Tseng Qingzong, Ulf Dittmer, Uwe Walschus, Valerio Mussi, Ved Sharma, Vytas Bindokas, Wilhelm Burger, Winfried Wurm, Xiao Chen, Zeljka Maglica.

27 Focus on Bioimage Informatics
In July 2012 Nature Methods issued a focus dedicated to the role of bioimage informatics in microscopy, the tools that are available for scientific image processing, and the challenges and opportunities in the field. The special issue features a large collection of articles discussing ImageJ, Fiji↑ and related projects↑, including:
  • [A] Albert Cardona, Pavel Tomancak: “Current challenges in open-source bioimage informatics”, Nature Methods, pp. 661—5, 2012. doi: 10.1038/nmeth.2082.
  • [B] Anne E Carpenter, Lee Kamentsky, Kevin W Eliceiri: “A call for bioimaging software usability”, Nature Methods, pp. 666—70, 2012. doi: 10.1038/nmeth.2073.
  • [C] Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri: “NIH Image to ImageJ: 25 years of image analysis”, Nature Methods, pp. 671, 2012. doi: doi:10.1038/nmeth.2089.
  • [D] 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: “Fiji: an open-source platform for biological-image analysis”, Nature Methods, pp. 676—82, 2012. doi: 10.1038/nmeth.2019.
  • [E] Kevin W Eliceiri, Michael R Berthold, Ilya G Goldberg, Luis Ibáñez, B S Manjunath, Maryann E Martone, Robert F Murphy, Hanchuan Peng, Anne L Plant, Badrinath Roysam, Nico Stuurmann, Jason R Swedlow, Pavel Tomancak, Anne E Carpenter: “Biological imaging software tools”, Nature Methods, pp. 697—710, 2012. doi: 10.1038/nmeth.2084.
A full announcement can be found on the Fiji news channel.
The following references are a small sample (particularly biased towards the life sciences) of the bibliography directly related to ImageJ, the standard in scientific image analysis. These publications include: 1) technical articles and books describing routines implemented in ImageJ, 2) research articles that have made extensive use of ImageJ as a scientific tool or 3) reviews that discuss ImageJ pertinently. A similar list is maintained on the Fiji↑ website.
To cite ImageJ one of the following references is possible (see FAQs):
  1. Rasband WS. ImageJ, U.S. National Institutes of Health, Bethesda, Maryland, USA, imagej.nih.gov/ij/, 1997—2012.
  2. Abràmoff MD, Magalhães PJ and Ram SJ. “Image Processing with ImageJ”, Biophotonics International, 11(7):36—42, 2004 (PDF) [67].
  3. Schneider CA, Rasband WS and Eliceiri KW. “NIH Image to ImageJ: 25 years of image analysis”, Nature Methods, pp. 671, 2012. doi: doi:10.1038/nmeth.2089 [C].
To cite Fiji↑:
  • Schindelin J et al. “Fiji: an open-source platform for biological-image analysis”, Nature Methods, pp. 676—82, 2012. doi: 10.1038/nmeth.2019 [D].
To cite this document:

ImageJ Related Publications

[1] A Cardona, S Saalfeld, P Tomancak, V Hartenstein: “Drosophila brain development: closing the gap between a macroarchitectural and microarchitectural approach”, Cold Spring Harbor Symposia on Quantitative Biology, pp. 235—48, 2009. doi: 10.1101/sqb.2009.74.037.

[2] A J Hand, T Sun, D C Barber, D R Hose, S MacNeil: “Automated tracking of migrating cells in phase-contrast video microscopy sequences using image registration”, Journal of microscopy, pp. 62—79, 2009. doi: 10.1111/j.1365-2818.2009.03144.x.

[3] A M Bell, K Parton, E Smith: “EarthTutor: An Interactive Intelligent Tutoring System for Remote Sensing”, American Geophysical Union, pp. 08, 2005.

[4] A Solé, J Mas, I Esteve: “A new method based on image analysis for determining cyanobacterial biomass by CLSM in stratified benthic sediments”, Ultramicroscopy, pp. 669—73, 2007. doi: 10.1016/j.ultramic.2007.01.007.

[5] Adam S Green, Paul R Ohmann, Nick E Leininger, James A Kavanaugh: “Polarization Imaging and Insect Vision”, The Physics Teacher, pp. 17, 2010. doi: 10.1119/1.3274352.

[6] Albert Cardona, Stephan Saalfeld, Stephan Preibisch, Benjamin Schmid, Anchi Cheng, Jim Pulokas, Pavel Tomancak, Volker Hartenstein: “An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy”, PLoS Biol , 2010. doi: 10.1371/journal.pbio.1000502.

[7] Simon Andrews, Jonathan Gilley, Michael P Coleman: “Difference Tracker: ImageJ plugins for fully automated analysis of multiple axonal transport parameters”, J Neurosci Methods, pp. 281-7, 2010. doi: 10.1016/j.jneumeth.2010.09.007.

[8] Anna Kirilova, Gina Lockwood, M Math, Perry Choi, Neelufer Bana, Masoom A Haider, Kristy K Brock, Cynthia Eccles, Laura A Dawson: “Three-dimensional motion of liver tumors using cine-magnetic resonance imaging”, Int J Radiat Oncol, pp. 1189—1195, 2008. doi: 10.1016/j.ijrobp.2007.11.026.

[9] Anne E Carpenter, Thouis R Jones, Michael R Lamprecht, Colin Clarke, In Han Kang, Ola Friman, David A Guertin, Joo Han Chang, Robert A Lindquist, Jason Moffat, Polina Golland, David M Sabatini: “CellProfiler: image analysis software for identifying and quantifying cell phenotypes”, Genome Biol, pp. R100, 2006. doi: 10.1186/gb-2006-7-10-r100.

[10] Arthur Edelstein, Nenad Amodaj, Karl Hoover, Ron Vale, Nico Stuurman: “Computer control of microscopes using μManager”, Curr Protoc Mol Biol, pp. Unit14.20, 2010. doi: 10.1002/0471142727.mb1420s92.

[11] Atsuko Kobayashi, Takumi Fujigaya, Masayuki Itoh, Takahisa Taguchi, Hiroshi Takano: “Technical note: a tool for determining rotational tilt axis with or without fiducial markers”, Ultramicroscopy, pp. 1—6, 2009. doi: 10.1016/j.ultramic.2009.08.007.

[12] B Choi, C Nelson, Y Tsunashima, P Balter: “Open source, ImageJ based, web accessible tool for treatment plan evaluation”, Med Phys, pp. 2477—2477, 2007. doi: 10.1118/1.2760991.

[13] Benjamin Schmid, Johannes Schindelin, Albert Cardona, Mark Longair, Martin Heisenberg: “A high-level 3D visualization API for Java and ImageJ”, BMC Bioinformatics 2010 11:274, pp. 274, 2010. doi: 10.1186/1471-2105-11-274.

[14] Brian A Irving, Judy Y Weltman, David W Brock, Christopher K Davis, Glenn A Gaesser, Arthur Weltman: “NIH ImageJ and Slice-O-Matic computed tomography imaging software to quantify soft tissue”, Obesity (Silver Spring), pp. 370—6, 2007. doi: 10.1038/oby.2007.573.

[15] C Igathinathane, LO Pordesimo, EP Columbus, WD Batchelor, SR Methuku: “Shape identification and particles size distribution from basic shape parameters using ImageJ”, Comput Electron Agr, pp. 168—182, 2008. doi: 10.1016/j.compag.2008.02.007.

[16] C Igathinathane, LO Pordesimo, WD Batchelor: “Major orthogonal dimensions measurement of food grains by machine vision using ImageJ”, Food Res Int, pp. 76—84, 2009. doi: 10.1016/j.foodres.2008.08.013.

[17] Cédric Messaoudi, Nicole Garreau de Loubresse, Thomas Boudier, Pascale Dupuis-Williams, Sergio Marco: “Multiple-axis tomography: applications to basal bodies from Paramecium tetraurelia”, Biol Cell, pp. 415—25, 2006. doi: 10.1042/BC20050097.

[18] Cédric Messaoudii, Thomas Boudier, Carlos Oscar Sanchez Sorzano, Sergio Marco: “TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy”, BMC Bioinformatics, pp. 288, 2007. doi: 10.1186/1471-2105-8-288.

[19] Charles A Lessman, Ravikanth Nathani, Rafique Uddin, Jamie Walker, Jianxiong Liu: “Computer-aided meiotic maturation assay (CAMMA) of zebrafish (Danio rerio) oocytes in vitro”, Mol Reprod Dev, pp. 97—107, 2007. doi: 10.1002/mrd.20530.

[20] Christof Karmonik, Michele York, Robert Grossman, Ekta Kakkar, Krutina Patel, Hani Haykal, David King: “An image analysis pipeline for the semi-automated analysis of clinical fMRI images based on freely available software”, Computers in biology and medicine , 2010. doi: 10.1016/j.compbiomed.2009.12.003.

[21] Christopher A Myrick: “A low-cost system for capturing and analyzing the motion of aquatic organisms”, J N Am Benthol Soc, pp. 101—109, 2009. doi: 10.1899/08-067.1.

[22] Clayton M Costa, Suann Yang: “Counting pollen grains using readily available, free image processing and analysis software”, Ann Bot, pp. 1005—10, 2009. doi: 10.1093/aob/mcp186.

[23] Daniel P Barboriak, Anthony O Padua, Gerald E York, James R Macfall: “Creation of DICOM—aware applications using ImageJ”, J Digit Imaging, pp. 91—9, 2005. doi: 10.1007/s10278-004-1879-4.

[24] Daniel Sage, Franck R Neumann, Florence Hediger, Susan M Gasser, Michael Unser: “Automatic tracking of individual fluorescence particles: application to the study of chromosome dynamics”, IEEE Trans Image Process, pp. 1372—83, 2005.

[25] David Hecker, Joachim Kappler, Alexander Glassmann, Karl Schilling, Wolfgang Alt: “Image analysis of time-lapse movies—a precision control guided approach to correct motion artefacts”, J Neurosci Methods, pp. 67—73, 2008. doi: 10.1016/j.jneumeth.2008.04.010.

[26] David J Barry, Cecilia Chan, Gwilym A Williams: “Morphological quantification of filamentous fungal development using membrane immobilization and automatic image analysis”, J Ind Microbiol Biotechnol, pp. 787—800, 2009. doi: 10.1007/s10295-009-0552-9.

[27] David Stepensky: “FRETcalc plugin for calculation of FRET in non-continuous intracellular compartments”, Biochem. Biophys. Res. Commun., pp. 752—8, 2007. doi: 10.1016/j.bbrc.2007.05.180.

[28] Delphine S A Beeckman, Geert Meesen, Patrick Van Oostveldt, Daisy Vanrompay: “Digital titration: automated image acquisition and analysis of load and growth of Chlamydophila psittaci”, Microsc. Res. Tech., pp. 398—402, 2009. doi: 10.1002/jemt.20694.

[29] Derick Lau, Anthony Seibert, David Gandara, Luko Laptalo, Este Geraghty, Christopher Coulon: “Computer-assisted image analysis of bronchioloalveolar carcinoma”, Clin Lung Cancer, pp. 281—6, 2005.

[30] Dilraj Grewal, Rajeev Jain, Gagandeep Singh Brar, Satinder Pal Singh Grewal: “Pentacam tomograms: a novel method for quantification of posterior capsule opacification”, Invest Ophthalmol Vis Sci, pp. 2004—8, 2008. doi: 10.1167/iovs.07-1056.

[31] E Iannuccelli, F Mompart, J Gellin, Y Lahbib-Mansais, M Yerle, T Boudier: “NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments”, Bioinformatics, pp. 696—7, 2010. doi: 10.1093/bioinformatics/btq013.

[32] E Meijering, M Jacob, J-C F Sarria, P Steiner, H Hirling, M Unser: “Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images.”, Cytometry. Part A : the journal of the International Society for Analytical Cytology, pp. 167—76, 2004. doi: 10.1002/cyto.a.20022.

[33] Eben Gering, Carter T Atkinson: “A rapid method for counting nucleated erythrocytes on stained blood smears by digital image analysis”, J Parasitol, pp. 879—81, 2004.

[34] Eckard Picht, Aleksey V Zima, Lothar A Blatter, Donald M Bers: “SparkMaster: automated calcium spark analysis with ImageJ”, Am J Physiol, Cell Physiol, pp. C1073—81, 2007. doi: 10.1152/ajpcell.00586.2006.

[35] Edmund Y Tong, Geoffrey C Collins, April E Greene-Colozzi, Julia L Chen, Philip D Manos, Kyle M Judkins, Joseph A Lee, Michael J Ophir, Farrah M Laliberte, Timothy J Levesque: “Motion-based angiogenesis analysis: a simple method to quantify blood vessel growth”, Zebrafish, pp. 239—43, 2009. doi: 10.1089/zeb.2008.0554.

[36] Emel Bulut, Bünyamin Sahin: “A new method of assessing the size of mandibular cysts on orthopantomograms: projection area fraction”, J Craniofac Surg, pp. 2020—3, 2009. doi: 10.1097/SCS.0b013e3181bd302e.

[37] Evan C Crawford, James K Mortensen: “An ImageJ plugin for the rapid morphological characterization of separated particles and an initial application to placer gold analysis”, Computers & Geosciences, pp. 347, 2009. doi: 10.1016/j.cageo.2007.11.012.

[38] F. Leymarie, M. D. Levine: “Fast raster scan distance propagation on the discrete rectangular lattice”, CVGIP: Image Understanding, pp. 84—94, 1992. doi: DOI: 10.1016/1049-9660(92)90008-Q.

[39] Fathima Shihana, Dhammika Menike Dissanayake, Nicholas Allan Buckley, Andrew Hamilton Dawson: “A Simple Quantitative Bedside Test to Determine Methemoglobin”, Ann Emerg Med , 2009. doi: 10.1016/j.annemergmed.2009.07.022.

[40] Fernán Federici, Lionel Dupuy, Laurent Laplaze, Marcus Heisler, Jim Haseloff: “Integrated genetic and computation methods for in planta cytometry”, Nature methods , 2012. doi: 10.1038/nmeth.1940.

[41] Michael J M Fischer, Sae Uchida, Karl Messlinger: “Measurement of meningeal blood vessel diameter in vivo with a plug-in for ImageJ”, Microvasc Res, pp. 258-66, 2010. doi: 10.1016/j.mvr.2010.04.004.

[42] Francesca Papadopulos, Matthew Spinelli, Sabrina Valente, Laura Foroni, Catia Orrico, Francesco Alviano, Gianandrea Pasquinelli: “Common tasks in microscopic and ultrastructural image analysis using ImageJ”, Ultrastruct Pathol, pp. 401—7, 2007. doi: 10.1080/01913120701719189.

[43] G Landini, G Perryer: “Digital enhancement of haematoxylin- and eosin-stained histological images for red-green colour-blind observers”, J Microsc, pp. 293—301, 2009. doi: 10.1111/j.1365-2818.2009.03174.x.

[44] Gary Chinga, Per Olav Johnsen, Robert Dougherty, Elisabeth Lunden Berli, Joachim Walter: “Quantification of the 3D microstructure of SC surfaces”, Journal of microscopy, pp. 254—65, 2007. doi: 10.1111/j.1365-2818.2007.01809.x.

[45] German Kilimnik, Abraham Kim, Junghyo Jo, Kevin Miller, Manami Hara: “Quantification of pancreatic islet distribution in situ in mice”, Am J Physiol Endocrinol Metab, pp. E1331—8, 2009. doi: 10.1152/ajpendo.00479.2009.

[46] H M Macdonald, D M L Cooper, H A McKay: “Anterior-posterior bending strength at the tibial shaft increases with physical activity in boys: evidence for non-uniform geometric adaptation”, Osteoporos Int, pp. 61—70, 2009. doi: 10.1007/s00198-008-0636-9.

[47] Ricardo Henriques, Mickael Lelek, Eugenio F Fornasiero, Flavia Valtorta, Christophe Zimmer, Musa M Mhlanga: “QuickPALM: 3D real-time photoactivation nanoscopy image processing in ImageJ”, Nat Methods, pp. 339-40, 2010. doi: 10.1038/nmeth0510-339.

[48] J C Grochowsky, L W Alaways, R Siskey, E Most, S M Kurtz: “Digital photogrammetry for quantitative wear analysis of retrieved TKA components”, J Biomed Mater Res Part B Appl Biomater, pp. 263—7, 2006. doi: 10.1002/jbm.b.30537.

[49] J Hegyi, V Hegyi, G Messer, P Arenberger, T Ruzicka, C Berking: “Confocal laser-scanning capillaroscopy: a novel approach to the analysis of skin capillaries in vivo”, Skin Res Technol, pp. 476—81, 2009. doi: 10.1111/j.1600-0846.2009.00393.x.

[50] Jason R Swedlow, Kevin W Eliceiri: “Open source bioimage informatics for cell biology”, Trends in Cell Biology, pp. 656—60, 2009. doi: 10.1016/j.tcb.2009.08.007.

[51] János Roszik, Duarte Lisboa, János Szöllosi, György Vereb: “Evaluation of intensity-based ratiometric FRET in image cytometry—approaches and a software solution”, Cytometry A, pp. 761—7, 2009. doi: 10.1002/cyto.a.20747.

[52] János Roszik, János Szöllosi, György Vereb: “AccPbFRET: an ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images”, BMC Bioinformatics, pp. 346, 2008. doi: 10.1186/1471-2105-9-346.

[53] Jennifer L West, Ian D Cameron: “Using the medical image processing package, ImageJ, for astronomy”, arXiv , 2006.

[54] Jérôme N Feige, Daniel Sage, Walter Wahli, Béatrice Desvergne, Laurent Gelman: “PixFRET, an ImageJ plug-in for FRET calculation that can accommodate variations in spectral bleed-throughs”, Microsc. Res. Tech., pp. 51—8, 2005. doi: 10.1002/jemt.20215.

[55] Joel B Sheffield: “ImageJ, a useful tool for biological image processing and analysis”, Microsc Microanal, pp. 200—201, 2007. doi: 10.1017/S1431927607076611.

[56] John D Gottsch, Olof H Sundin, Erik V Rencs, David G Emmert, Walter J Stark, Clement J Cheng, Gregory W Schmidt: “Analysis and documentation of progression of Fuchs corneal dystrophy with retroillumination photography”, Cornea, pp. 485—9, 2006. doi: 10.1097/01.ico.0000178726.11693.14.

[57] Jonas G Wilson-Leedy, Rolf L Ingermann: “Development of a novel CASA system based on open source software for characterization of zebrafish sperm motility parameters”, Theriogenology, pp. 661—72, 2007. doi: 10.1016/j.theriogenology.2006.10.003.

[58] Jonathan Popko, Adelaide Fernandes, Dora Brites, Lorene M Lanier: “Automated Analysis of NeuronJ Tracing Data”, Cytom Part A, pp. 371—376, 2009. doi: 10.1002/cyto.a.20660.

[59] K Moodley, H Murrell: “A colour-map plugin for the open source, Java based, image processing package, ImageJ”, Computers & Geosciences, pp. 609—618, 2004. doi: 10.1016/j.cageo.2004.03.017.

[60] V. Kaynig, T. Fuchs, J.M. Buhmann: “Neuron geometry extraction by perceptual grouping in ssTEM images”, , pp. 2902 -2909, 2010.

[61] Kerry M Brown, Duncan E Donohue, Giampaolo D'Alessandro, Giorgio A Ascoli: “A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks”, Neuroinformatics, pp. 343—60, 2005. doi: 10.1385/NI:3:4:343.

[62] Kevin M Schartz, Kevin S Berbaum, Robert T Caldwell, Mark T Madsen: “WorkstationJ: workstation emulation software for medical image perception and technology evaluation research”, Medical Imaging 2007: Image Perception, pp. 49, 2007. doi: 10.1117/12.708482.

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