Human and Murine Retinal OCT Analysis and Display

The Iowa Reference Algorithms are a suite of algorithms for quantitative analysis of human and murine 3-D retinal Optical Coherence Tomography images. 

It was developed by the members of the Retinal Image Analysis Laboratory (see below).

The Iowa Reference Algorithms are compatible with Windows XP, and 7 and above. Mac-OS, Linux, Unix, and other operating systems are currently not supported. The mouse OCT layer segmentation algorithm requires approximately 48GB of RAM. They are compatible with SD-OCT image data from all widely-available clinical OCT scanners, including Heidelberg Spectralis, Topcon 1000 and 2000, Zeiss Cirrus, and Bioptigen. In some cases a research agreement is required from the manufacturer of your OCT scanning device to enable export of raw image data from the OCT scanner, please contact the respective OCT manufacturer if/as needed. Potentially useful, Zeiss provides “research browser” software to convert their custom .dcm to .img, and Heidelberg provides software to convert .e2e to .vol .  

The Iowa Reference Algorithms are for investigational purposes only, and are not approved for clinical care nor by the the US Food and Drug Agency.

Retinal Image Analysis Laboratory

Retinal Image Analysis Laboratory is home to an interdisciplinary group of researchers from the Stephen A. Wynn Institute for Vision Research, and the Departments of Ophthalmology and Visual Sciences, Electrical and Computer Engineering, Biomedical Engineering, all at the University of Iowa. This group is an integral part of the Iowa Institute for Biomedical Imaging. The Lab has been very active in developing retinal SD-OCT analysis suites for quantitative retinal analysis.

Iowa Reference Algorithm Stable Releases contain the following:

  • OCTExplorer – for easy viewing and annotations of scans and resulting analyses
  • OCTSegmenter – this module can be called from the OCT-Explorer and segments eleven retinal surfaces in macula-centered OCT volumes. See our publications for more info.
  • Manual

We plan to release software providing additional retinal OCT analysis capabilites in the months and years ahead.

See below for Release Information and Download links.

Citing the Iowa Reference Algorithm

The Iowa Reference Algorithms were developed by Kyungmoo Lee, Michael D. Abramoff, Mona Garvin, and Milan Sonka, as well as other lab members. The underlying n-dimensional graph-based multi-surface segmentation is based on the graph-theoretical and algorithmic work of Xiaodong Wu.

By using the Iowa Reference Algorithms, you are obliged to:

  • Refer to it as “The Iowa Reference Algorithms (Retinal Image Analysis Lab, Iowa Institute for Biomedical Imaging, Iowa City, IA)
  • Reference at least three of the following papers in any publications that use the Iowa Reference Algorithms in any way by choosing the papers that are most relevant to your work.
    • Abramoff MD, Garvin M, Sonka M. Retinal Imaging and Image Analysis. IEEE Reviews in Biomedical Engineering, 3, 169-208, 2010. doi:10.1109/RBME.2010.2084567
    • Kang L, Wu X, Chen DZ, Sonka M. Optimal Surface Segmentation in Volumetric Images – A Graph-Theoretic Approach. IEEE Transactions on Pattern Analysis and Machine Intelligence Volume 28:119-134, 2006. doi:10.1109/TPAMI.2006.19
    • Garvin MK, Abramoff MD, Wu X, Burns TK, Russell SR, Sonka M. Automated 3-D Intraretinal Layer Segmentation of Macular Spectral-Domain Optical Coherence Tomography Images. IEEE Trans Med. Imaging, 28, 9, 1436-47, 2009. doi:10.1109/TMI.2009.2016958
    • Antony B, Abramoff MD, Tang L, Ramdas WD, Vingerling JR, Jansonius NM, Lee K, Kwon YH, Sonka M, Garvin MK. Automated 3-D method for the correction of axial artifacts in spectral-domain optical coherence tomography images. Biomed Opt Express 2(8):2403-16, 2011. doi:10.1364/BOE.2.002403
    • Optical Coherence Tomography Analysis Based Prediction of Humphrey 24-2 Visual Field Thresholds in Patients With Glaucoma. Guo Z, Kwon YH, Lee K, Wang K, Wahle A, Alward WLM, Fingert JH, Bettis DI, Johnson CA, Garvin MK, Sonka M, Abràmoff MD. Invest Ophthalmol Vis Sci. 2017 Aug 1;58(10):3975-3985. doi: 10.1167/iovs.17-21832. PMID: 28796875

Free

The current release of Iowa Reference Algorithms is available free of charge for research use. By accepting the licensing agreement, you agree that you will only use it for non-commercial research. Commercial licenses are available; for more information, please contact uirf@uiowa.edu.

Not Free

The Retinal Image Analysis Laboratory has developed and continues developing a growing suite of SD-OCT image analysis software tools and modules. Some of these – after careful validation – will be added to the free research-only section provided for download on this page. Others, however, will only be available to our direct research collaborators with licensing governed by special license agreements between the University of Iowa and the second parties.

Similarly, commercial licenses are available.

Please contact uirf@uiowa.edu for additional information about software not included in the free release.

Manuals

 The User Manual pdf is also included in the download.

Support

Development was supported, in part, by the following funding sources:

  • NIH-NIBIB R01-EB044640
  • NIH-NEI R01-EY018853
  • NIH-NEI RO1-EY019112
  • Research to Prevent Blindness
  • NIH-NEI EY017066
  • Arnold and Mabel Beckman Initiative for Macular Research

Release Information

Pre-Release 5.0.0 (beta)

Version 5.0.0 (beta) improvements over versions 3.8.0 and 4.0.0 (beta)
  • Improved 11 retinal layer segmentation of macular OCT scans (additional subretinal virtual space)
  • 5.x layer segmentation algorithm including user interaction is fundamentally different from 3.x and 4.x versions.
  • Output of version 5.x is compatible with version 3.8 and later.
  • Nightly validation of segmentation output
  • User manual update
  • Requirements: 64-bit Microsoft Windows or Mac OS X, 6 GB RAM for non-cystic and 20 GB RAM for cystic Zeiss OCT scans (200 x 1024 x 200 voxels)
  • (Does not include OCT Explorer)

Current Release 3.8.0 (stable)

Version 3.8.0 improvements over version 3.6
  • Due to many requests, the 3.x versions will be maintained in the future. Currently this is the stable version.
  • Improved 10 retinal layer segmentation of macular and ONH OCT scans
  • All segmentation parameters have been made device independent for increased robustness across scanners.
  • Aligned coordinate system for data representation with all other versions (switched y- and z- axes from version 3.6)
    • ​Output of version 3.8.0 is compatible with the output from 4.0.0 (beta).
  • Bug fix for the circular/elliptical grid regions starting/ending 90 or 270 degrees
  • User manual update
  • Nightly validation of segmentation output
  • Requirements: Microsoft Windows x64, 4 GB RAM
(History of older releases)

Download

Please fill the information form below to request access to software download links.

Definitions:
 
Provider - Institution providing the Original Material:
        The University of Iowa Research Foundation
Provider's Scientists:
        Ipek Oguz
        Xiaodong Wu
        Milan Sonka
 
Recipient - Institution receiving the Original Material:
        Institution employing person requesting download: xxxxx
 
Recipient's Scientist(s): xxxxx
 
Person requesting download: xxxxx
 
Software: Iowa Reference Algorithms, including:
        RATS_MM
        RATS_LOGISMOS
        All which are partially described in:
Kang L, Wu X, Chen DZ, Sonka M. Optimal Surface Segmentation in Volumetric Images - A Graph-Theoretic Approach. IEEE Transactions on Pattern Analysis and Machine Intelligence Volume 28:119-134, 2006. doi:10.1109/TPAMI.2006.19
Yin Y, Zhang X, Williams R, Wu X, Anderson DD, Sonka M. LOGISMOS - Layered Optimal Graph Image Segmentation of Multiple Objects and Surfaces: Cartilage Segmentation in the Knee Joint. IEEE Transactions on Medical Imaging (2010) vol. 29 (12) pp. 2023-37. 
doi:10.1109/TMI.2010.2058861
Oguz I, Zhang H, Rumple A, Sonka M. RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI. Journal of Neuroscience Methods (2014) vol. 221 pp. 175 – 182.
doi:10.1016/j.jneumeth.2013.09.021

Patents
United States Patent 7,995,810, "System and Methods for Image segmentation in N- dimensional space". Inventors: K Li, X Wu, DZ Chen, M Sonka
And any other patents and applications claiming priority to the above.
 
Terms and Conditions of this Agreement
1. The Effective Date of this Software Transfer Agreement is the date electronically agreed to by Recipient's Scientist as part of this license.
2. The Software is the property of Provider and is to be used by Recipient solely for research purposes only at Recipient's institution and only under the direction of the Recipient's Scientist(s). The Software may not be used in the diagnosis or treatment of patients and Recipient and Recipient Scientist(s) may not use Software in a manner which generates income or remuneration for Recipient and Recipient Scientist(s).
3. The Recipient's Scientist(s) agrees not to transfer or provide the Software to anyone else at Recipient's institution or any third party without the prior written consent of Provider. The Software being used is further restricted to a single computer. Recipient's Scientist shall refer any request for the Software to Provider.
4. No rights are provided to Recipient under the patents above or any patents, patent applications, copyrights, trade secrets or other proprietary rights of Provider. In particular, no rights are provided to use the Software or any related intellectual property of Provider for making, using, or distributing the intellectual property, material or derivatives thereof in exchange for any form of compensation or reimbursement. However, nothing in this paragraph or any other section of this Agreement shall be construed to interfere with, restrict or otherwise limit Recipient's rights to receive or spend the grant proceeds under any Prime Award and Provider encourages Recipient to explore state, Federal and internal funding opportunities using the Software.
5. The provision of the Software to Recipient shall not alter any preexisting right to the Software, including the customary rights granted to the federal government or non-profit foundations.
6. Any Software delivered pursuant to this Agreement is understood to be experimental in nature. PROVIDER MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED. THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE MATERIAL WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK OR OTHER PROPRIETARY RIGHTS.
7. Except to the extent prohibited by law, Recipient assumes all liability for damages which may arise from its use, storage or disposal of the Software. Provider will not be liable to Recipient for any loss, claim or demand made by Recipient, made against Recipient or by any other party, due to or arising from the use of the Software by the Recipient, except to the extent permitted by law when caused by the gross negligence or willful misconduct of Provider.
8. Software is being provided to Recipient at no cost.
9. Recipient agrees that Provider and Provider's Scientist(s) shall receive appropriate recognition in any publication or presentation resulting from the use of agreed upon Software.
10. Recipient agrees to use the Software in compliance with all applicable statues and regulations, including, for example, Export Control.
 
Institution: The University of Iowa Research Foundation
Address: 200 S. Capitol Street, 2660 University Capitol Centre, Iowa City, IA 52242-5500
Authorized Official: Zev Sunleaf
Title: Executive Director
 
 

Read Terms Agreement

Definitions:
 
Provider - Institution providing the Original Material:
        The University of Iowa Research Foundation
Provider's Scientists:
        Ipek Oguz
        Xiaodong Wu
        Milan Sonka
 
Recipient - Institution receiving the Original Material:
        Institution employing person requesting download: xxxxx
 
Recipient's Scientist(s): xxxxx
 
Person requesting download: xxxxx
 
Software: Iowa Reference Algorithms, including:
        RATS_MM
        RATS_LOGISMOS
        All which are partially described in:
Kang L, Wu X, Chen DZ, Sonka M. Optimal Surface Segmentation in Volumetric Images - A Graph-Theoretic Approach. IEEE Transactions on Pattern Analysis and Machine Intelligence Volume 28:119-134, 2006. doi:10.1109/TPAMI.2006.19
Yin Y, Zhang X, Williams R, Wu X, Anderson DD, Sonka M. LOGISMOS - Layered Optimal Graph Image Segmentation of Multiple Objects and Surfaces: Cartilage Segmentation in the Knee Joint. IEEE Transactions on Medical Imaging (2010) vol. 29 (12) pp. 2023-37. 
doi:10.1109/TMI.2010.2058861
Oguz I, Zhang H, Rumple A, Sonka M. RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI. Journal of Neuroscience Methods (2014) vol. 221 pp. 175 – 182.
doi:10.1016/j.jneumeth.2013.09.021

Patents
United States Patent 7,995,810, "System and Methods for Image segmentation in N- dimensional space". Inventors: K Li, X Wu, DZ Chen, M Sonka
And any other patents and applications claiming priority to the above.
 
Terms and Conditions of this Agreement
1. The Effective Date of this Software Transfer Agreement is the date electronically agreed to by Recipient's Scientist as part of this license.
2. The Software is the property of Provider and is to be used by Recipient solely for research purposes only at Recipient's institution and only under the direction of the Recipient's Scientist(s). The Software may not be used in the diagnosis or treatment of patients and Recipient and Recipient Scientist(s) may not use Software in a manner which generates income or remuneration for Recipient and Recipient Scientist(s).
3. The Recipient's Scientist(s) agrees not to transfer or provide the Software to anyone else at Recipient's institution or any third party without the prior written consent of Provider. The Software being used is further restricted to a single computer. Recipient's Scientist shall refer any request for the Software to Provider.
4. No rights are provided to Recipient under the patents above or any patents, patent applications, copyrights, trade secrets or other proprietary rights of Provider. In particular, no rights are provided to use the Software or any related intellectual property of Provider for making, using, or distributing the intellectual property, material or derivatives thereof in exchange for any form of compensation or reimbursement. However, nothing in this paragraph or any other section of this Agreement shall be construed to interfere with, restrict or otherwise limit Recipient's rights to receive or spend the grant proceeds under any Prime Award and Provider encourages Recipient to explore state, Federal and internal funding opportunities using the Software.
5. The provision of the Software to Recipient shall not alter any preexisting right to the Software, including the customary rights granted to the federal government or non-profit foundations.
6. Any Software delivered pursuant to this Agreement is understood to be experimental in nature. PROVIDER MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED. THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE MATERIAL WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK OR OTHER PROPRIETARY RIGHTS.
7. Except to the extent prohibited by law, Recipient assumes all liability for damages which may arise from its use, storage or disposal of the Software. Provider will not be liable to Recipient for any loss, claim or demand made by Recipient, made against Recipient or by any other party, due to or arising from the use of the Software by the Recipient, except to the extent permitted by law when caused by the gross negligence or willful misconduct of Provider.
8. Software is being provided to Recipient at no cost.
9. Recipient agrees that Provider and Provider's Scientist(s) shall receive appropriate recognition in any publication or presentation resulting from the use of agreed upon Software.
10. Recipient agrees to use the Software in compliance with all applicable statues and regulations, including, for example, Export Control.
 
Institution: The University of Iowa Research Foundation
Address: 200 S. Capitol Street, 2660 University Capitol Centre, Iowa City, IA 52242-5500
Authorized Official: Zev Sunleaf
Title: Executive Director