Developer(s) | ADCIS French company |
---|---|
Initial release | 1996 (24 years ago) |
Stable release | 4.4.0 / 6 October 2017 (2 years ago) |
Written in | C sharp, C++ |
Operating system | Windows |
Type | Image processing |
License | Proprietary commercial software |
Website | www.adcis.net/en/home/ |
Stereological analysis. The stereological analysis was performed, using the computer assisted stereology software newCAST (Visiopharm A/S). The computer selected the fields of view (FOV) by systematic, random sampling within the ROI (Fig. 3).The sampling fraction varied according to the size of the ROI and the lymphocytic density.
The Aphelion Imaging Software Suite is a set of computer programs for image processing and image analysis. It includes three base products: Aphelion Lab, Aphelion Dev, and Aphelion SDK.
The Aphelion software product can be used to prototype applications using the graphical user interface. It provides a set of tools for programmers which have to develop software with image analysis needs.
- 5Notes and references
- 5.1Other references
Applications[change | change source]
The Aphelion Imaging Software Suite is used by students, researchers, engineers, and software developers in application domains requiring image processing and computer vision,[1][2] such as:
- security (surveillance, object tracking)
- remote sensing
- quality control for the industry and inspection applications
- life sciences (medicine and biology)
- earth science (geology)
- theory (image processing, machine learning and optimization)
Specifications[change | change source]
![Stereology Stereology](http://www.adcis.net/en/Products/Vertical/images/StereologyAnalyzer1.png)
Aphelion Dev Graphical User Interface version 4.x: (1) Task Bar, (2) Image Display, (3) Macro editing window/Function window, (4) Charts (a profile is displayed in this example), (5) Image Gallery, (6) Measurement grid.
All products of the Aphelion Imaging Software Suite can be run on PC equipped with Windows (Vista, 7, 8, 8.1,[3] or 10) 32 or 64 bits.[4]An online help[5] and video tutorials are available to the user.[6]
Software extensions[change | change source]
Below is a list of Aphelion optional extensions:[7][8]
- 3D Image Processing and 3D Image Display: A set of extensions to display and process 3D images. The 3D display extension is based on the VTK software product.[9]
- 3D Skeletonization: Extension to compute the 3D skeleton.
- Image Registration: Image registration extension to register images coming from different acquisition devices.
- Classification Tools: Classification extension including a « Fuzzy Logic » (fuzzy logic classification),« Neural Networks » (classification based on neural networks), and « Random Forest » (classification based on random forests, derived from the R software product)
- Kriging: Specific extension to remove image noise using geostatistics techniques.
- Camera interface drivers and microscope interface software
- Virtual Image Capture and Virtual Image Stitcher: Two software products to capture mult-field images and stitch them into one single and very large image in the fields of optical and electron microscopy (image stitching).
- Stereology Analyzer: Software to analyze a very large image using stereology. This extension is mainly used in the field of biology on images acquired by a scan microscope.
- VisionTutor: Online image processing course including all the theory and application macro commands that are compatible with Aphelion.
The Aphelion user can add his/her own macro-commands in the user interface[7] that have been automatically recorded to process a batch of images. He/she can also add plugins and libraries in the GUI that have been developed outside the Aphelion environment.[10]
Software versions[change | change source]
Below is a table providing release dates of the Aphelion software product:
Software release[11] | Release date |
Aphelion 1.0 | 1995 |
Aphelion 2.0 first official version | 1996 |
Aphelion 2.1 | 1996–1997 |
Aphelion 2.2 | 1997 |
Aphelion 2.3 | 1998–1999 |
Aphelion 3.0 | 1999–2000 |
Aphelion 3.1 | December 2001 |
Aphelion 3.2a-f | 2001–2004 |
Aphelion 3.2g | March 2004 |
Aphelion 3.2h | November 2004 |
Aphelion 3.2i | March 2006 |
Aphelion 3.2j | October 2008 – 2012 |
Aphelion 4.0.0 | July 2009 |
Aphelion 4.0.5 | December 2009 |
Aphelion 4.0.6 | May 2010 |
Aphelion 4.0.7 | August 2010 |
Aphelion 4.0.8 | October 2010 |
Aphelion 4.0.9 | February 2011 |
Aphelion 4.0.10 | April 2011 |
Aphelion 4.1.0 | October 2011 |
Aphelion 4.1.1 | April 2012 |
Aphelion 4.1.2 | November 2012 |
Aphelion 4.2.0 | February 2013 |
Aphelion 4.2.1 | January 2014 |
Aphelion 4.3.0 | October 2014 |
Aphelion 4.3.1 | December 2014 |
Aphelion 4.3.2 | September 2015 |
Aphelion 4.4.0 | October 2017 |
GUI of a previous version of Aphelion (version 3.2j).
Notes and references[change | change source]
- ↑'Aphelion application fields'. adcis.net. Retrieved 5 November 2015.
- ↑'Aphelion application fields videos'. adcis.net. Retrieved 5 November 2015.
- ↑'What is new in Aphelion 4.3 release'. adcis.net. Retrieved 18 November 2015.
- ↑'Aphelion Dev overview'. adcis.net. Retrieved 18 November 2015.
- ↑'Help documents'. adcis.net. Retrieved 5 November 2015.
- ↑'ADCIS (Advanced Concepts in Imaging Software) products videos'. adcis.net. Retrieved 5 November 2015.
- ↑ 7.07.1'Official Aphelion Dev brochure (2015)'(pdf). adcis.net. Retrieved 19 November 2015.
- ↑'Software extensions brochures'. adcis.net. Retrieved 18 November 2015.
- ↑Legland, David (March 2009). 'Solutions logicielles pour le traitement d'images' (in fr) (pdf). INRA (Institut National de la Recherche Agronomique). http://www7.inra.fr/vh/pflcepia/uploads/docs/softsImage.pdf. Retrieved 25 February 2016.
- ↑'Aphelion user guide (Loading a macro as an Aphelion plugin)'(pdf). adcis.net. Retrieved 5 November 2015.
- ↑'Aphelion version and changes history'. adcis.net. Retrieved 5 November 2015.
Other references[change | change source]
Miscellaneous[change | change source]
- 'Image analysis software list'. peipa.essex.ac.uk. Retrieved 19 November 2015.
- 'Aphelion 2006 advertising'(pdf). AdvancedImagingPro.com. Retrieved 19 November 2015.
Materials science applications[change | change source]
- Hénault, Éric (2006). 'Method of Automatic Characterization of Inclusion Population by a SEM-FEG/EDS/Image Analysis System'. JEOL NEWS41 (73): 22–24. http://www.jeolusa.com/NEWSEVENTS/JEOLNEWSMagazine/tabid/275/Default.aspx. Retrieved 14 November 2015.A coupling was carried out between a field-emission scanning electron microscope (JEOL, JSM-6500F), an energy-dispersive spectrometer (EDS) (PGT, detector SDD SAHARA) and image analysis software (APHELION).
- Hellal, Fatah et al. (February 2000). 'Diffusion du carbone lors de la décomposition de l'austénite en ferrite et en graphite dans une fonte à graphite sphéroïdal' (in fr). Canadian Journal of Physics77 (9). doi:10.1139/p99-037.
- Geandier, G. et al. (December 2003). 'Residual stresses in alumina-chromium composites: micromechanical analysis and study by X-ray diffraction'. Revue de Métallurgie100 (12): 1163–1172. doi:10.1051/metal:2003185.
- Moreaud, Maxime (10 April 2007) (in fr) (pdf). Nanotomographie. http://cmm.mines-paristech.fr/Nanomines/Rapports/NanoTomov1.pdf. Retrieved 22 February 2016.[...] une solution complète d'alignement des projections et de reconstruction tomographique 3D a été développée et intégrée à la plateforme Aphelion.
[ [...] a complete projection alignment and 3D reconstruction plug-in was developed and integrated to Aphelion.]
- Bizet, L. et al. (2004). 'Serial sections through a continuous fiber-reinforced polymer composite'. Image Analysis and Stereology23 (3): 167–176. doi:10.5566/ias.v23.p167-176.However, they can be defined after simple morphological transformations on the digitized images of the microstructure: a closing is made on the fiber phase of the yarn by using the Aphelion software.
- Yotte, S. et al. (2004). 'PMMC cluster analysis'. Computer Modeling in Engineering & Sciences5 (2): 171–188. doi:10.3970/cmes.2004.005.171.
- Blacher, Silvia et al. (14 July 2004). 'Image analysis of X-ray microtomograms of Pd–Ag/SiO
2 xerogel catalysts supported on Al
2O
3 foams.'. Colloids and Surfaces A: Physicochemical and Engineering Aspects241 (1-3): 201–206. doi:10.1016/j.colsurfa.2004.04.006. - Fall, A. et al. (November 2001). 'Characterization of Mixing in a Stirred Tank by Planar Laser Induced Fluorescence (PLIF)'. 4th International Symposium on Mixing in Industrial Processes79 (8): 876–882. doi:10.1205/02638760152721073.
- Léonard, Angélique et al. (15 June 2005). 'Image analysis of X-ray microtomograms of soft materials during convective drying: 3D measurements'. Journal of Microscopy218 (3): 247–252. doi:10.1111/j.1365-2818.2005.01485.x.Specific programs were developed using Aphelion 3.2f (Adcis S.A.) and Matlab software, with image analysis toolbox version 6.0 from Mathworks (Natick, MA).
- Lambert, Jérôme et al. (February 2005). 'Extraction of relevant physical parameters from 3D images of foams obtained by X-ray tomography'. Colloids and Surfaces A: Physicochemical and Engineering Aspects263 (1-3): 295–302. doi:10.1016/j.colsurfa.2005.01.002.
Life sciences applications[change | change source]
- Poulletier de Gannes, Florence (June 2006). 'Effect of GSM-900 RFR on HSP expression in brain immune cells' in 28th Annual Meeting of the BEMS. . hal-00161897, version 1. Retrieved on 5 November 2015.The level of heat shock protein expression was estimated using image analysis (Aphelion software).
- Jost, Maud et al. (15 May 2006). 'Earlier Onset of Tumoral Angiogenesis in Matrix Metalloproteinase-19–Deficient Mice'. Cancer Research (66). doi:10.1158/0008-5472.CAN-05-4315.The ratio between the surface of bisbenzimide staining and the surface of specific immunostaining was measured by using a software Aphelion 3.2 from Adcis (Herouville Saint Clair, France).
- Van't Hof, Rob et al. (October 2004). 'Identification of biphenylcarboxylic acid derivatives as a novel class of bone resorption inhibitors'. Journal of Bone and Mineral Research (19). doi:10.1359/jbmr.2004.19.10.165. https://www.researchgate.net/publication/8357603_Identification_of_Biphenylcarboxylic_Acid_Derivatives_as_a_Novel_Class_of_Bone_Resorption_Inhibitors. Retrieved 5 November 2015.The area resorbed was quantified by Image Analysis using custom software developed using Aphelion ActiveX objects (ADCIS).
- Herlin, Paulette (4–8 July 2005). 'Avantages d'une quantification à basse résolution de la vascularisation intratumorale' (pdf) in 9th conference of the French Microscopy Society (French: Société Française des Microscopies) (SFµ). . Retrieved on 25 November 2015.Une routine de traitement d'images, développée dans l'environnement du logiciel boîte à outils Aphelion (ADCIS) permet de donner une appréciation objective du degré de vascularisation moyen et maximal de la tumeur.
[An image analysis macro-command, developed in the Aphelion (ADCIS) toolbox software, allows to appreciate objectively the mean and maximum grades of tumor vascularisation.]
- Le Maire, Sophie et al. (2005). 'Caractérisation par analyse d'images de l'angiogenèse sur des coupes histologiques' (in fr). Group for study of signal and image analysis (French: GRETSI (Groupe d'Études du Traitement du Signal et des Images)). http://hdl.handle.net/2042/14096. Retrieved 22 February 2016.Les logiciels utilisés pour réaliser ce travail sont les suivants : (a) APHELION v.3.2 pour le traitement d'images 2D, la reconstruction 3D et les mesures 2D et 3D, [...]
[Softwares used to accomplish this work are: (a) APHELION v.3.2 for 2D image analysis, 3D reconstruction, and 2D and 3D measurements, [...] ]
- Ghazi, Kamelia et al. (16 November 2012). 'Hyaluronan Fragments Improve Wound Healing on In Vitro Cutaneous Model through P2X7 Purinoreceptor Basal Activation: Role of Molecular Weight'. PLOS ONE. doi:10.1371/journal.pone.0048351.Percentage of wound area was measured using Aphelion Dev image processing and analysis software developed by ADCIS S.A.
- Hatem, I. et al. (June 2003). 'Cartilage and bone segmentation in vertebra images'. Transactions of the American Society of Agricultural and Biological Engineers (46). doi:10.13031/2013.15436.
- Kriston-Vizi, Janos et al. (2004). 'Biometrical approaches for mandarin leaf image analysis'. Applied Ecology and Environmental Research (2): 119–134. doi:10.15666/aeer/02119134.For image analysis the Aphelion software package was used made by Adcis SA and AAI Inc.
Earth science applications[change | change source]
- Lebourg, Thomas et al. (2004). 'Influence of morphological characteristics of heterogeneous till formations on the mechanical behaviour by using image and statistical analysis'. Engineering geology (73): 37–50. doi:10.1016/j.enggeo.2003.11.004. https://www.researchgate.net/publication/228416061_Influence_of_morphological_characteristics_of_heterogeneous_moraine_formations_on_their_mechanical_behaviour_using_image_and_statistical_analysis. Retrieved 5 November 2015.
- Lebourg, Thomas et al. (October 2003). 'Morphological Characteristics of Till Formations in Relation with Mechanical Parameters'. Mathematical geology35 (7): 835–852. https://link.springer.com/article/10.1023%2FB%3AMATG.0000007782.78685.a3.
- Gauchat, K. et al. (2006). 'Cristal Size Distribution (CSD) of garnets as function of metallographic grade and composition in black marls of the Nufenen zone' (pdf). Geophysical Research Abstracts8. http://meetings.copernicus.org/www.cosis.net/abstracts/EGU06/08269/EGU06-J-08269.pdf.The 2D garnet distributions and garnet shapes were determined using the Aphelion image analysis program
- Riss, Joëlle (6 February 2003). 'Taille et Forme des cristaux de quartz dans une géode du forage EPS1 de Soultz-sous-Forêts' in 25th conference of the French Stereology Society. .
- A., Hosni (13–15 October 2003). 'Coupled THM modelling of the stimulated permeable fractures in the near well at the Soultz-sous-Forêts site (France)' in Geoproc 2003, International Conference on Coupled T-H-M-C Processes in Geosystems. 2 : 665–670. DOI:10.1016/S1571-9960(04)80116-2.
Theory applications[change | change source]
- Hanbury, Allan; Serra, Jean (2002) (pdf). A 3D-polar coordinate colour representation suitable for image analysis. University of Technology, Vienna, Austria. PRIP-TR-77. http://www.cmm.mines-paristech.fr/~serra/notes_internes_pdf/NI-230.pdf. Retrieved 5 November 2015.Software already used by the author which implement cylindrically shaped colour models include: Matlab release 12.1, Aphelion 3.0, Optimas 6.1 and Paint Shop Pro 7.
- Brambor, Jaromír (11 July 2006). Algorithmes de la morphologie mathématique pour les architectures orientées flux [Mathematical morphology algorithms for flow oriented architectures] (pdf) (Ph.D. in mathematical morphology) (in French). School of Mines of Paris (Mines ParisTech). p. 80. Retrieved 23 February 2016.
Other websites[change | change source]
Retrieved from 'https://simple.wikipedia.org/w/index.php?title=Aphelion_(software)&oldid=6486194'
These scripts are designed to assist with performing unbiased stereology using the Fiji distribution of ImageJ.
Credits
These scripts were written or modified, as noted, by Theresa Swayne, Ph.D., Columbia University, New York, NY, USA. This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. If you use the material, please read the license and give credit appropriately.
The original Multipurpose Grid macro was written by Aleksandr Mironov.
Installation
For jython scripts (.py):
Use the Fiji distribution of ImageJ. Plain ImageJ does not support Jython.
To run the script from anywhere on your computer, open Fiji,
File > Open
, select the script, and click Run
.To install so that the command appears in the ImageJ menu, follow instructions here.
For ImageJ1 macros (.ijm):
Use Fiji or plain ImageJ.
To run the macro from anywhere on your computer, open Fiji,
File > Open
, select the script, and click Run
.To install so that the command appears in the ImageJ menu, follow instructions here.
For Batch commands (.txt):
Use Fiji or plain ImageJ.
Note that
batch apply grid.txt
requires the macro Multipurpose_gridMod.ijm
to be installed in the plugins folder!- Open the Batch Macro command (
Process > Macro...
). - Set the
Input
folder to the folder containing the images you want to process. All files in the folder will be processed. - Set the
Output
folder to a different folder where you would like the results to be saved. - Click
Open
and select the .txt file. - Click
Process
.
Sample workflow
Here is one way to use these scripts.
- Open a slide scanner image using VSI Reader, and create a grid of ROIs.
- Use
random_ROI.py
to select a subset of the tissue for analysis. - Use
batch apply grid.txt
to overlay a non-destructive counting grid on the set of images. - During counting, if you have a large area containing many points, use
cross_count.ijm
to count black crosses within the area.
Limitations
- To change the number of fields or grid characteristics you need to edit the scripts.
- Cross counting works only with black crosses, and assumes there is no black in the image.
Disclaimer
I have tested these at the time of uploading. If you find a bug, please contact me.
Contact
Theresa Swayne, Ph.D., Confocal and Specialized Microscopy Shared Resource, Columbia University