Martin Caon

Multi-organ segmentation of CT images using statistical region merging

Segmentation is one of the key steps in the process of developing anatomical models for calculation of safe medical dose of radiation for children. This study explores the potential of the Statistical Region Merging segmentation technique for tissue segmentation in CT images. An analytical criterion allowing for an automatic tuning of the method is developed. The experiments are performed using a data set of 54 images from one patient, demonstrating the validity of the proposed criterion. The results are evaluated using the Jaccard index and a measure of border error with tolerance which addresses, application-dependant, acceptable error. The outcome shows that the technique has a great potential to become a method of choice for segmentation of CT images with an overall average boundary precison, for six representative tissues, equal to 0.937.

Full-body CT segmentation using 3D extension of two graph-based methods: a feasibility study

The paper studies the feasibility of using 3D extensions of two state-of-the-art segmentation techniques, the Statistical Region Merging (SRM) method and the Efficient Graph-based Segmentation (EGS) technique, for automatic anatomy segmentation on clinical 3D CT images. The proposed methods are tested on a dataset of 55 images. The test is for segmentation of eight representative tissues (lungs, stomach, liver, heart, kidneys, spleen, bones and the spinal cord) which are vital for accurate calculation of radiation doses. The results are evaluated using the Dice index, the Hausdorff distance and the Ht index, a measure of border error with tolerance t pixels addressing the uncertainty in the ground truth. The outcome shows that the 3D-SRM method outperforms 3D-EGS and has a great potential to become the method of choice for segmentation of full-body CT images. Using 3D-SRM, the average Dice index, the Hausdorff distance across the 8 tissues, and the H2 were0.89, 12.5 mm and0.93, respectively.

Plagiarism in scientific/medical physics publishing.

Recently (August 2007) the IOMP Publications Committee email list (which consists of the editors of about 14 Medical Physics journals in several languages) has been discussing plagiarism in submitted manuscripts and published articles. Concurrently so has the email list of the World Association of Medical Editors (WAME). One could be forgiven for thinking that plagiarism has recently become a problem. Plagiarism is unacceptable, unethical, dishonest and, particularly in peer-reviewed scientific publishing where the scientific literature is keenly searched for ideas, precedents and results that confirm or contradict your own gets noticed. Some organisations (eg IOP publishing) have policies and procedures that their editorial staff follow when plagiarism is alleged. The Committee on Publication Ethics (COPE), have published flowcharts that describe for editors what to do in cases of suspected plagiarism. The COPE website also has descriptions of examples of detected plagiarism and their recommended course of action. Plagiarism is taken very seriously, will cause the editors involved to invest a lot of their time investigating incidents, and has dire consequences for the author(s) involved. In short, the authors are asked to explain and if a case of plagiarism is considered to have occurred, eventually everyone is informed of the outcome. That is, all of the authors, perhaps their superiors, perhaps their institutions, the manuscript’s reviewers, the authors who were plagiarised, perhaps the worldwide email community of editors and eventually the scientific community when the journal involved publishes a corrigendum or a retraction of the article. Then there are the sanctions.

March 2013 editorial: operational statistics for the APESM Journal (Jan 2012-Feb 2013).

APESM is quite a different entity in 2013 than it was when I last wrote about the state of the journal in 2009 [1]. Among other things, from 2010, the journal has been published by Springer and since 2009 the number of published articles has doubled and the number of submissions has almost tripled. Springer’s online manuscript submission and tracking system makes it easy to extract summary data, some of which is presented below. In 2008, APESM volume 31 published 39 scientific articles. Fifty-three manuscripts were submitted in that calendar year of which 42 were eventually published. Fifty-two articles were published in volume 35. In calendar year 2012, 134 manuscripts were submitted of which 25 (so far) have been published with 85 (so far) having been rejected. The current high rate of rejection is a reflection both of the rigour of the peer review process and of the diversity of submitted manuscripts. The increase in submissions may be attributed to the increased visibility of APESM since being published by Springer, and in turn this is largely due to the journal’s website and the growth in the use of the internet. Furthermore, accepted manuscripts are published on the website as soon as they are ready (and they may be cited with the digital object identifier-DOI). Hence, rather than waiting for the paper copy of the issue to be assembled, such articles are immediately visible to internet searches.

Osmoles, osmolality and osmotic pressure: clarifying the puzzle of solution concentration.

Nurses are routinely involved in the collecting and testing of urine and plasma, dialysis, the administration of intravenous fluids and the treatment of osmolar disorders, all of which require an understanding of solution concentration.This article discusses the various ways in which the concentration of solutions are stated, how they differ and why the different ways of expressing concentration are useful in human physiology. It also explains the similarities and differences between the terms used to describe solution concentration: tonicity, percentage concentration, density, specific gravity, molarity, osmolarity, osmolality and osmotic pressure.The terms osmolarity, osmolality and osmotic pressure appear routinely in textbooks used in undergraduate nursing courses but often are used incorrectly as synonyms.The usefulness and the appropriate context to use the different ways of expressing solution concentration is discussed. Osmolality (or osmolarity) should be used instead of osmotic pressure to describe the movement of water between compartments while the use of osmotic pressure should be reserved for situations where filtration and osmosis are operating together.

Automating the Segmentation of Medical Images for the Production of Voxel Tomographic Computational Models

Radiation dosimetry for the diagnostic medical imaging procedures performed on humans requires anatomically accurate, computational models. These may be constructed from medical images as voxel-based tomographic models. However, they are time consuming to produce and as a consequence, there are few available. This paper discusses the emergence of semi-automatic segmentation techniques and describes an application (iRAD) written inMicrosoft Visual Basic that allows the bitmap of a medical image to be segmented interactively and semi-automatically while displayed inMicrosoft Excel. iRAD will decrease the time required to construct voxel models.

Gaming the impact factor: where who cites what, whom and when

of scholars, is not supported by the scientific community and is being used by people outside of those communities for purposes for which it is not intended, then yes. Let me ask another question. Are institutions/people who use the impact factor inappropriately for purposes for which it was not intended, also gaming it? Should such behaviour be subject to sanction? Gaming the impact factor is not like plagiarising some text and including it in an article that you submit for publication, nor like an athlete taking performance enhancing drugs. Such behaviours are wrong, illegal and exemplify misconduct. Rather it may be likened to “optimising” your website so that it achieves a higher ranking on Google’s search engine results. Or to paying to Boost your post on “facebook” and so make it appear higher in your News Feed and on Instagram. It’s a victimless crime, we all expect it and accept it. We are mature enough to be aware that it does happen yet ignore it anyway. I know that you know that there are many shortcomings to the impact factor but we seem to tacitly agree to forgive them. There is no watchdog to oversee the legitimate operation of the impact factor (but Thomson Reuters does monitor citation behaviour) or indeed to sanction those who use it for unintended purposes. Hence it is possible to arrange the arithmetic to optimise the outcome for a particular journal. That is, the impact factor rises if the “numerator” can be increased while minimising the “denominator”.

Operational statistics for the APESM journal (2014–2016)

APESM editorial and review effort is managed from Australia, New Zealand and North America by members of the sponsoring scientific College (ACPSEM), publication effort is in the Netherlands by Springer while online management and tracking of manuscripts is undertaken from India. In 2015 there were over 7800 institutions worldwide with access to APESM electronically via online deals with Springer. Manuscripts may arrive from any country and an approximate measure of the global visibility of APESM can be gained from the number of countries from which manuscripts are submitted for consideration and by the number of countries from which the reviewers are drawn. A manuscript is deemed to have come from the country of residence of the first listed author. During the 3 year period 2014–2016 manuscripts were received from a total of 53 countries. Table 1 column 8 lists the number of different countries from which manuscripts were received in each year. The top twelve source countries for APESM manuscripts are listed in Table 2. While authors from 15 European countries submitted manuscripts to APESM, the majority came from Asian countries. The manuscripts are sent to reviewers who are recently published researchers in the field and these are drawn from a great many countries (see Table 1). The top twelve source countries for reviewers are presented in Table 2, column 2. Unsurprisingly, reviewers from English-speaking countries are most commonly used. However reviewers are also often drawn from India, China and Iran. While not amongst the top twelve, many reviewers were also from Germany, Spain and Greece [2]. The influence or impact of an article is sometimes equated to the number of times it has been cited [3], but another index is how often it is read as measured by the It may be of interest and instructive to authors who submit research articles to a scientific journal to see a summary of some of the statistics about manuscripts submitted to the APESM journal. It is with the intent of improving the transparency of the processes that I publish these operational statistics for APESM for the 3 year period 2014–2016. It can be seen from Table 1 that between 2014 and 2016, the number of manuscripts submitted and published in APESM has increased. This growth continues the trend that was apparent the last time that operational statistics were reported in 2013 for APESM [1]. Soon after submission, manuscripts are checked for the quality of English expression, scientific structure, plagiarism, duplicate publication, and consideration is given to the scientific novelty of the reported findings. As a result of this scrutiny, between 35 and 40% of manuscripts were rejected by the editors without being sent to reviewers (see Table 1, column 3). In addition, some submitted manuscripts that are deemed to be not yet ready for review, are returned to the authors for modification prior to being accepted for review as we do not wish to waste reviewers’ time with manuscripts that are under-prepared. We don’t keep records of this that are good enough to be definitive, but the number is probably greater than 30%. Some of these may ultimately be rejected without review, if the modification is inadequate.

There are too many medical physics journals

What I really mean is that there are too many unscientific ‘‘scientific journals’’. There must be. Why else do I get so many spam emails requesting that my esteemed person make a valuable contribution to their Journal(s) which publish in fields that I have no expertise in? Why else, if not the existence of too much capacity, would journals need to beg for content from potential authors who demonstrably have no knowledge of the Journal’s field (unless of course, they want authors to pay for publication)? There are so many that I will restrict the discussion below to the Medical Physics journals—even though I have not yet been spammed by a Medical Physics journal. I define a Medical Physics journal as one that has the term ‘‘medical physics’’ (not necessarily in English) in the title, or has both the words ‘‘physics’’ (or ‘‘physical’’) and ‘‘medical’’ (or ‘‘biomedical’’ or ‘‘medicine’’) in the title, or as one whose website states that they publish ‘‘medical physics’’ articles (for example the ‘‘Red Journal’’, BPEX, R&EB, RPT, IJRR). However the three journals: Physiological Chemistry and Physics and Medical NMR; Magnetic Resonance Materials in Physics, Biology, and Medicine; EPJ Nonlinear Biomedical Physics (est. 2013)— which may or may not have supplanted the now ceased BioMed Central published Nonlinear Biomedical Physics (est. 2007)—and medical journals with the term ‘‘physical medicine’’ in their title, were not considered to be Medical Physics journals. Any appropriate journal published by a national association of medical physicists qualifies for inclusion. I know that it could be argued that nuclear medicine, health physics, biomedical engineering, radiation protection, dosimetry, medical imaging, radiology, oncology, biophysics and other areas of scientific endeavour overlap with medical physics. Well argue away, but I have drawn the line as above. Strangely, ‘‘medical physics’’ is not a term that is used to describe a subject area or subject category by Scimago Journal Ranking or by Thomson Reuters Journal Citation Reports or used by them to classify scientific journals. Hence the term is not applied by those organisations to any of the Journals that I have identified. As far as I can ascertain there are 32 Medical Physics journals (or journals that publish medical physics articles) and a further two that have ceased to publish (Table 1). All of them have websites and post their tables of contents and abstracts online, and this is how I found them. Ten of the journals publish articles in a language that is not English. Be advised that the publishers of three of the listed journals feature on Jeffrey Beall’s list of predatory publishers [1]. Prior to 1980 there were 5 Medical Physics journals (including this one). By 1990 there were 8, by 2000 there were 14 and by 2010 the number had risen to 24. Ten more have established since then. It is clear that the number of medical physics journals, the frequency of their issues and the number of published medical physics articles has been increasing [2]. And that the rate of increase has been increasing. This is not surprising as the number of medical physicists has risen in response to the development of new radiotherapy treatments and the introduction of new diagnostic equipment and the introduction of modern medicine into developing countries [3]. In turn these developments have been driven by the research efforts of the equipment manufacturers and the users of the new equipment and by medical physics students/registrars completing their & Martin Caon martin.caon@flinders.edu.au

Abbreviations, initialism and acronyms: their use in medical physics (THUMP)

Manuscripts that are submitted to this journal (APESM) always contain abbreviations and acronyms. In fact despite existing advice to the contrary, the trend amongst authors seems to be to increase their use [1]. This fashion has progressed to the stage where they are now overused. We ask: why the fad (WTF)? Abbreviations are short forms of existing words designed to save time and to take up less space in situations where there is insufficient space to write the entire words. Initialisms may be considered to be a subset of abbreviations where the abbreviation consists of using the first letters of the words (ACPSEM for example). Acronyms (in turn) may be considered to be a subset of initialisms where the abbreviation can be pronounced as if it was a word (PET for example). However, the words acronym and initialism are often used as synonyms. Truncations are another form of abbreviation where a word is shortened to its first syllable or few letters, for example linear accelerator is linac, and formula translating is Fortran. These truncated words work well as new words because they are easy to pronounce, their etymology is clear and their meaning is intuitive. When abbreviation results in unpronounceable terms which are counter-intuitive, they do not work so well. The advice to authors of scientific writing is: ‘‘Abbreviations should also be avoided whenever possible.’’ and ‘‘Avoid jargon and acronyms’’ [2]. ‘‘Avoid unfamiliar abbreviations.....’’ [3]. ‘‘Additionally, authors should avoid uncommon abbreviations....’’ [4]. Okay (OK), sometimes it is acceptable to abbreviate, particularly when it makes your writing easier to read. In this regard, Mack’s advice is sound: ‘‘A good rule for abbreviations is to put the reader first. Ask yourself: Will the abbreviationmake the sentence easier to read, orwill it confuse the reader?’’ [4]. If the answer to the first part of the question is no, then don’t use that abbreviation. If the abbreviation is an acronym that cannot be pronounced or is unpleasant to say, making it necessary to read each letter separately with athletic enunciation, then don’t use that abbreviation. It is acceptable to use abbreviations in the following circumstances. When they are: Standard abbreviations of units of measurement (Gy, kV, mAs); When they are symbols in a mathematical formula; Personal titles (Ms, Dr, Prof.); The designated symbols for chemical elements; Abbreviated names of familiar organisations (ICRP, IAEA, NRPB, ARPANSA); In headings and lables for figures and tables (where the saving of space is truly useful); Industry standard acronyms that can be pronounced like words (kerma, DICOM, ROMP, PACS). Furthermore an acronym that forms a unique aggregation of letters can be useful as a web search keyword. This is particularly true for the name of an organisation (but be aware that ACPSEM is also used by the Association of Chartered Physiotherapists in Sports and Exercise Medicine!). Producers of computer software are keen on this form of unique acronym for their products. In addition, some abbreviations work because the phrase they replace is difficult (and tedious) to read if it is used often, while the acronym rolls off the tongue. For example ASCII instead of ‘‘American National Standard Code for Information Interchange’’. Or a phrase has been invented by a nerd, and it would make little sense if used in a sentence as the intended meaning of the words, when used together, is not apparent (e.g. URL for uniform resource locator, HTML for hyper-text mark up language, DOI for digital object identifier). Perhaps the phrases should never have been used in the first place. & Martin Caon martin.caon@flinders.edu.au