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How to refer to the software?

How to reference the software

Proper referencing of the software when publishing scientific results is a prerequisite for using the software. This important since we need to prove to granting organisations that the Software is used and contributes to the scientific community. It also helps new users to find the software.

A reference should encompass both the name of the software, and a suitable publication. When in doubt, please send an email to einar@heiberg.se or put reference [4] which is the generic reference for image analysis in Segment. This paper describes Segment and is open-access paper.

Examples of possible formulations for different usage are:

  • Generic use of the software for various image processing tasks. Image Analysis was done using the freely available software Segment version 1.8 R1145 (http://segment.heiberg.se) [4].

  • Using the software to determine LV mass/EF/volumes etc (in automatic or manual mode) should be referenced as something like left ventricular mass measured using Segment v1.x (http://segment.heiberg.se) [1]. Where [1] is a reference to the 2005 Computers in Cardiology short paper. Another example of formulation could be Image analysis was performed off-line using the freely available analysis software (Segment; http://segment.heiberg.se) [1] . Reference [4] could also very well be used for this purpose.

  • Using the software for (semi) automatic quantification of infarct size/transmurality etc should be referenced to either [2] or [3] (as below) depending on which algorithm has been used. If the new and better weighted algorithm has been used then the reference should be to [3]. Suggested phrasing is something like infarct size were determined using Segment v1.x (http://segment.heiberg.se) [2]/[3].

  • Flow quantification should be referred to as [4].

  • Quantification of LV mass in SPECT images should be referenced to with reference [5].

  • Quantification defect sizes in SPECT images should be referenced to with reference [6].

  • Usage of the fusion module should be referenced as [7]. Please not that this will be replaced by a peer reviewed paper when such one is available.

  • Segmentation of myocardium at risk from T2 STIR imaging should be referred to as [8].

  • Segmentation of myocardium at risk from cine delayed enhancement should be referenced to as [9]

  • Measurement of endocardial extent should be referenced to as [10].

  • Creating polar plots should be referred to as [11].

These references are subject to change as submitted manuscript(s) are accepted for publication. Always check this web-page before submitting a paper.

Note that referencing the software is manditory also for abstracts to scientific conferences. If shortage of space, at least reference the software as something like:

  • Images was analysed using the freely available software Segment (http://segment.heiberg.se).

In extreme shortage of space, such as conferences where the word limit is <350 words then reference may be omitted in the abstract text, but should be included in the oral presentation and / or poster.

References

[1] E. Heiberg, L. Wigström, M. Carlsson, A. F. Bolger, and M. Karlsson, Time Resolved Three-dimensional Automated Segmentation of the Left Ventricle. In Proceedings of IEEE Computers in Cardiology 2005(32), pp. 599-602, Lyon, France, 2005.

[2] E. Heiberg, H. Engblom, J. Engvall, E. Hedstrom, M. Ugander, and H. Arheden, Semi-automatic quantification of myocardial infarction from delayed contrast enhanced magnetic resonance imaging, Scand Cardiovasc J 39(5) pp. 267-75, 2005.

[3] E. Heiberg, M. Ugander, H. Engblom, M. Götberg, G. K. Olivecrona, D. Erlinge, and H. Arheden, Automated quantification of myocardial infarction from MR images by accounting for partial volume effects: animal, phantom, and human study, Radiology 246(2) pp. 581-8, 2008.

[4] E. Heiberg, J. Sjögren, M. Ugander, M. Carlsson, H. Engblom, and H. Arheden, Design and Validation of Segment - a Freely Available Software for Cardiovascular Image Analysis, BMC Medical Imaging, 10:1, 2010.

[5] H. Soneson, J. F. Ubachs, M. Ugander, H. Arheden, and E. Heiberg, An improved method for automatic segmentation of the left ventricle in myocardial perfusion SPECT, J Nucl Med 50(2) pp. 205-13, 2009.

[6] H. Soneson, H. Engblom, E. Hedstrom, F. Bouvier, P. Sorensson, J. Pernow, H. Arheden, and E. Heiberg, An automatic method for quantification of myocardium at risk from myocardial perfusion SPECT in patients with acute coronary occlusion, J Nucl Cardiol, In Press.

[7] M. Ugander, H. Soneson, E. Heiberg, H. Engblom, J. v. d. Pals, D. Erlinge, and H. Arheden, A novel method for quantifying myocardial perfusion SPECT defect size by co-registration and fusion with MRI - an experimental ex vivo imaging pig heart study. In Proceedings of Scand Cardiovasc J, vol 42 suppl(42 Suppl), p 47, Malmö, 2008.

[8] M. Carlsson, J. F. Ubachs, E. Hedstrom, E. Heiberg, S. Jovinge, and H. Arheden, Myocardium at risk after acute infarction in humans on cardiac magnetic resonance: quantitative assessment during follow-up and validation with single-photon emission computed tomography, JACC Cardiovasc Imaging 2(5) pp. 569-76, 2009.

[9] P. Sorensson, E. Heiberg, N. Saleh, F. Bouvier, K. Caidahl, P. Tornvall, L. Ryden, J. Pernow, and H. Arheden, Assessment of myocardium at risk with contrast enhanced steady-state free precession cine cardiovascular magnetic resonance compared to single-photon emission computed tomography., J Cardiovasc Magn Reson, In press.

[10] H. Engblom, M. B. Carlsson, E. Hedstrom, E. Heiberg, M. Ugander, G. S. Wagner, and H. Arheden, The endocardial extent of reperfused first-time myocardial infarction is more predictive of pathologic Q waves than is infarct transmurality: a magnetic resonance imaging study, Clin Physiol Funct Imaging 27(2) pp. 101-8, 2007.

[11] P. A. Cain, M. Ugander, J. Palmer, M. Carlsson, E. Heiberg, and H. Arheden, Quantitative polar representation of left ventricular myocardial perfusion, function and viability using SPECT and cardiac magnetic resonance: initial results, Clin Physiol Funct Imaging 25(4) pp. 215-22, 2005.
 


Segment homepage, last modified 2010-08-09.