Usage of Drishti around the world

Graham Davis
Here are a couple of papers which use and acknowledge Drishti. It was also used in the BBC’s “The One Show”, which you can find here: http://www.youtube.com/watch?v=FXkQz9fOafU.
Quantitative high contrast X-ray microtomography for dental research.
Quantification of residual dentine thickness following crown preparation.

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Alan Boyde
To: Robert Hill; GR Davis; David Mills
Cc: Tomas Zikmund tomas.zikmund@ceitec.vutbr.cz (tomas.zikmund@ceitec.vutbr.cz); Professor Tim Cox
Subject: JOA 12226 on line this AM
the paper is on line
http://onlinelibrary.wiley.com/doi/10.1111/joa.12226/full

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Farah Ahmed,
I think we have over 10 publications this year between Dan and myself.. I'll ask him to get back to you as soon as possible..
Rebecca Summerfield R.Summerfield@nhm.ac.uk to drishti-user-g.
In addition to the 10 Dan and Farah have published this year, I am working on 3 publications that should be out before the end of the year, I gave a talk at Society of Electron Microscopy Tomography One day conference in December (Down the Microscope: The successes and limitations of Micro-CT and developing methodologies for comparative and confocal microscopy studies), and will be presenting a poster at IMC 2014.
I will send on the full details to you once they have been accepted/taken place.
Also drishti features (work by Dan and myself) heavily in this new NHM video on art, nature and imaging in science (http://www.nhm.ac.uk/nature-online/art-nature-imaging/).

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Martin Turner martinturner13@googlemail.com

All,
Totally agree - Drishti is one of our stable tools for the x-ray and neutron tomography. We have had two sesions focussing on Drishti in the last year within our show-and-tell sessions.
http://tinyurl.com/STFCVisSem

Also looking forward to seeing people at ToScA in September.

And a note the CCPi (Collaborative Computational Project in Tomographic Imaging, http://www.ccpi.ac.uk/) network (email ccpi@stfc.ac.uk to join) is now supporting the conference by sponsoring the Poster Competition so please enter :-)
http://www.nhm.ac.uk/research-curation/science-facilities/analytical-imaging/imaging/tosca-symposium/poster/index.jsp

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Harris Morrison
to drishti-user-g.

Tim,
I thought I'd posted this to you and Ajay before but now starting to wonder, especially given that I'd not checked it and now see that the person who submitted it didn't mention Drishti/Ajay in their description!!

https://www.flickr.com/photos/bhforguk/8703368427/

British Heart Foundation video of a infarct damaged heart, didn't win but Highly Commended and Supporter Favourite. This was published last year and got a gazillion re-runs around the world. Hopefully that should be added to the bibliography if it hasn't already.

PhD write up of Eve Anderson showing X-gal to examine LacZ reporter gene activity within the Sonic Hedgehog (Shh) genomic region. Been used in various internal seminars and a poster competition abroad but I forget where but can ask. (Movies and stills)

Oh, here's a new'ish one where the PI and student were looking at eyes, cataracts, etc.

http://dmm.biologists.org/content/7/6/711.full

They're a few biggish one but there are a million more images.

Cheers,
Harris

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aodhan.b@gmail.com aodhan.b@gmail.com

Hi Ajay,
Just a few conference talks in the autumn that we've used Drishti in to add to the bibliography list.
• Streng, M., Butler, A. D., & Garwood, R. J. 2014. It’s a brachiopod, it’s a coral, it’s a brachiopod – an enigmatic middle Cambrian organism adapted to reef-like environments? (Talk; Given by Michael Streng) 4th International Palaeontological Congress, Mendoza, Argentina.
• Butler, A. D., Garwood, R. J., Streng, M.,Lowe, T., & Holmer, L. E. 2014. Shedding light on the tommotiid stem-brachiopod transition with multi-scalar X-ray computed tomography. (Talk; Given by Aodhan Butler) 4th International Palaeontological Congress, Mendoza, Argentina.

Cheers
Aodhán

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Sherry.Mayo@csiro.au

to drishti-user-g.

Hi Ajay (& Tim)
As per Tim’s request, here are links to two of my papers citing Drishti.
http://www.scientific.net/MSF.654-656.2322
http://www.sciencedirect.com/science/article/pii/S1047847710001139

I’m teaching at the CLS summer school next week – mainly about X-TRACT, but they’ve also asked me to give them an introduction to Drishti. I hope this will help spread the Joy of Drishti a bit further afield. However it would be really great if I could get an outline of the sequence of things you (Ajay) typically go through when you run a Drishti workshop (e.g. with people following along on their own computers) as from my recollection of such a workshop it would be a pretty good template to follow for the CLS student. Mainly I just need a list of the topics you cover for newbies. I have an afternoon for the workshop so a fair bit of time.
Anton Maksimenko has some cool animations of IMBL (synchrotron) data most of the recent ones of which (in the last year) are made using Drishti. Check out his youtube page – https://www.youtube.com/user/antonmxx Sherry

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Bernhard Ruthensteiner
Dear Ajay,
sorry for my delayed reply concerning the support for the Drishti continuation.
I can offer only one paper (where Dristhi is somewhat undervalued): http://www.frontiersinzoology.com/content/10/1/44/abstract
Here some more reasoning:

• I’m producing mico-CT ( http://www.zsm.mwn.de/x-ray.htm (e.g. here 3 Drishti, 2 Amira, no VGS images)) (and physical section) data sets. Most of my „customers“ routinely apply Drishti for volume rendering. In quite some respects it is superior to the costly commercial standard volume rendering VG Studio Max.
  
• Drishti is part of 3D visualization courses and workshops. Attached here programs of such workshops and one photograph (Thomas Schwaha explaining segmentation at the Vienna Vetmed).
  
• The computation center of Munich runs a high-end visualization center ( http://www.lrz.de/services/v2c_de/ ), where Drishti is the main application for volume rendering ( https://www.lrz.de/services/v2c_en/software_en/vr-software_lrz/ ).
  
• For myself Drishti somewhat like the “daily bread” for dealing with data sets and it seems very difficult to do without.
  
  Accordingly, Drishti has become a standard tool for data examination in scientific fields such as biology or geosciences. Me and numerous scientists in the in these fields in Germany are highly interested in continuation of support for and development of this software.
  Please let me know if you would like to get additional information or receive this in a more formal style.
  All the best,
  3 Attachments
  Preview attachment ThSch-SegPaint.JPG
  Preview attachment DZG FG Morphologie Workshop From voxels to models - Second circular letter.pdf
  Preview attachment Virtual Palaeontology workshop.pdf
  

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Timothy Cox
to me, drew.whitehouse

Hi Drew & Ajay
Attached is a list of publications of ours that have used Drishti - some of these I have sent before but thought it easier to include all. There are a host of others in the works as well so will of course update the list in due course. Of those published so far, there have been four journal covers. I believe I had sent Ajay two of these previously so only attach the last two here (if you need better resolution I can send - just didn’t want to jam up your Inbox unnecessarily). Drishti was also critical for us getting one of our recent NIH grants and a private foundation grant (if you need grant titles let me know). It really has been instrumental in streamlining and increasing the efficiency of our work and images generated with Drishti are always the centerpiece of presentations to potential donors visiting the Institute. It is also a dream for students to use - much more user friendly that various commercial software. In total, I have ~8 folks in my lab (give or take a few) that use Drishti on a regular basis and I also use it as a core software in our Tomography facility, so encourage all external users (more than a dozen other research groups) of our facility to utilize it also.

On somewhat related matters, we have developed some of our own software here for shape analysis that I would love my student/new post doc to try to have as a plug-in for Drishti, so with any luck we will see if that is possible this year. In addition, we have a large funding opportunity here that I think may be able to be accessed for developing Drishti or another software for more automated segmentation/phenotyping if you guys have any interest of extending your support outside Oz. I am also peripherally involved with the NIDCR FaceBase program which is meant to be accumulating craniofacial data (image and other types) for ‘sharing’ with the craniofacial community. They have struggled to date with knowing how to share large tomographic datasets (ie. they were ill-prepared for the size of the datasets and how people might want to access them). Personally I think they should look at some of the tools you guys have developed. There are pots of money available within this program as well and perhaps some opportunity to work with the new coordinating ‘Hub’ team to implement online data viewing and sharing - given the coordinating team has just changed hands (ie. a good time to ‘strike’).

On an aside note, I mentioned to Ajay last year that we’d love to have him visit Seattle at some point to see our workflow, deficiencies, areas of need (or desire!) for Dristhi, and perhaps to do a mini-workshop for my group and other external users of our facility and other interested parties. I am, as usual, still hoping to find time to put a proposal together for this but I have at least had considerable expression of interest from the folks at the Friday Harbor Laboratories (the University’s marine biology campus in the San Juan Islands). But I am happy to extend that invitation to each of you (and Tim) as an opportunity to introduce Voluminous and Prayog and other VizLab activities over here. At minimum, would either of you consider coming through Seattle perhaps on the way back from ToScA this year? (I am considering going myself even though it is right over the start of the school year here (and so run the risk of death by wife) - but at minimum will send one of my lab)
Cheers
Tim

Publications with Drishti

Zovein, A.C., Turlo, K.A., Ponec, R.W., Lynch, M.R., Chen, K.C., Hofmann, J.J., Cox, T.C., Gasson, J.C., & Iruela-Arispe, M.L. (2010) Vascular remodeling of the vitelline artery initiates extra-vascular emergence of hematopoietic clusters. Blood 116(18):3435-3444. PMID: 20699440.
**Figure 1E – selected for Issue Cover
Wiseman, A., Cox, T.C., Paranjpe, A., Flake, N.M., Cohenca, N. & Johnson, J.D. (2011) Efficacy of sonic and ultrasonic activation combined with rotary instrumentation and positive pressure irrigation for removal of calcium hydroxide on mesial canals of mandibular molars: a micro-tomographic study. Journal of Endodontics 37(2):235-238. PMID: 21238809.
*Vissers, L.E.L.M., * Cox, T.C., *Maga, A.M., Short, K.M., Wirdajaja, F., Janssen, I.M., Jehee, F., Bertola, D., Liu, J., Yagnik, G., Sekiguchi, K., Kiyozumi, D., van Bokhoven, H., Marcelis, C., Cunningham, M.L., Anderson, P.J., Boyadjiev, S., Passos-Buenos, M-R., Veltman, J.A., Smyth, I., Buckley, M.F., & Roscioli, T. (2011) Heterozygous mutations of FREM1 are associated with an increased risk of isolated metopic craniosynostosis in humans and mice. PLoS Genetics 7(9): e1002278. doi:10.1371/journal.pgen.1002278. PMID: 21931569.
*authors contributed equally to this work.
Slavotinek, A.M., Baranzini, S.E., Schanze, D., Labelle-Dumais, C., Short, K.M., Chao, R., Yahyavi, M., Bijlsma, E.K., Chu, C., Musone, S., Wheatley, A., Kwok, P-Y., Marles, S., Li, C., Fryns, J-P., Maga, A.M., Hassan, M.G., Gould, D.B., Madireddy, L., Cox, T.C., Smyth, I., Chudley, A.E., Zenker, M. (2011) Manitoba-Oculo-Tricho-Anal (MOTA) syndrome is caused by mutations in FREM1. Journal of Medical Genetics. 48:375-382. PMID: 21507892.
Purushothaman, R., Cox, T.C., Maga, A.M. & Cunningham, M.L. (2011) Midfacial abnormalities of newborn Fgfr1P250R/+ and Fgfr2S252W/+ mouse models of Pfeiffer and Apert syndromes. Birth Defects Research Part A: Clinical and Molecular Teratology. 91(7):603-609. PMID: 21538817.
**Image selected for Issue Cover
Yamamura, B., Cox, T.C., Heddaya, B., Flake, N., Johnson, J.D. & Paranjpe, A. (2012) Comparing canal transportation and centering ability of EndoSequence and Vortex rotary files using micro-computed tomography. Journal of Endodontics 38:1121-1125. doi:10.1016/j.joen.2012.04.019. PMID: 22794219.
Siebert, J.R., Smith, K.J., Cox, L.L., Glass, I.A. & Cox, T.C. (2013) Microtomographic analysis of lower urinary tract obstruction. Pediatric and Developmental Pathology 16:405–414. doi:10.2350/13-08-1359-OA.1. PMID 23977847.
**Figure 7 – selected for Issue Cover
AllenPress press release: “New Scanning Techniques May Aid in Diagnosing Lower Urinary Tract Obstruction” (http://allenpress.com/node/975)
Cox, T.C., Luquetti, D.V. & Cunningham, M.L. (2013) Perspectives and challenges in advancing research into craniofacial anomalies. American Journal of Medical Genetics Part C (Seminars in Medical Genetics): Craniofacial Anomalies – Models, Mechanisms, and Management 163C:213–217. doi: 10.1002/ajmg.c.31383. PMCID: 3983849.
**Image selected for Issue Cover
McRay, B., Cox, T.C., Cohenca, N., Johnson, J., & Paranjpe, A. (2014) A micro-computed tomography-based comparison of the canal transportation and centering ability of ProTaper Universal and WaveOne rotary files. Quintenessence International 45: 101-108. doi:10.3290/j.qi.a30998.
Cox, T.C., Camci, E.D., Vora, S., Luquetti, D.V. & Turner, E.E. (2014) The genetics of auricular development and malformation: new findings in model systems driving future directions for microtia research. European Journal of Medical Genetics in press. (invited review).

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Kieran Short via anu.edu.au
to Ajay, Tim

Kieran Short & Bob Kao, Winners of Wellcome Image Awards 2011
Ian Smyth, Winner of Wellcome Image Awards 2011

Short KM et al., Spatial mapping and quantification of developmental branching morphogenesis. Development. 2013 Jan 15;140(2):471-8. doi: 10.1242/dev.088500. Epub 2012 Nov 28.

.. a video you guys rendered of one of my datasets from the development paper.. https://www.youtube.com/watch?v=vLa0l4X50Wk

Seriously -- this should be entered into the Wellcome Image awards too. It could win. Ajay, it looks like your handywork.

Short, KM, et al., 2014. Global Quantification of Tissue Dynamics in the Developing Mouse Kidney. Developmental Cell 29, 188–202, April 28, 2014.

You probably already have my 2010 Kidney international paper/ref on file.

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Nik Tatarnic
to me, Tim
Hi Ajay and Tim,
Here are a couple of papers where I've used Drishti. (There will be more once I get my collaborator to pull his finger out!)

I also have a series of conference presentations (all variations on the same thing):
Entomological Society of Canada, 3-7 November 2012, Edmonton Alberta:
Tatarnic, N.J. Sexual mimicry and paragenital divergence between sympatric species of traumatically inseminating plant bug.
Entomological Society of America: 11-14 November 2012, Knoxville Tennessee:
Tatarnic, N. J. Interspecies sexual conflict: Evidence of interspecies sexual mimicry in a sympatric pair of traumatically inseminating insects.
AND
Tatarnic, N. J. Sympatry, sexual conflict and traumatic insemination in the Pacific.
Australian Entomological Society, 25-28 November 2012:
Tatarnic, N.J. Sexual mimicry and paragenital divergence between sympatric species of traumatically inseminating plant bug.

Traumatic Insemination in Terrestrial Asthropods


I think I speak for others when I say that I'm incredibly grateful for the work Ajay has done with creating Drishti. It's a fantastic resource and it's amazing that it is open source.
Cheers,
NIk

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Carole Burrow
to Tim, me
Hi Tim, Ajay
The work for our talk at AESC2014 this week used Drishti (hey Tim?), pdf attached, abstract ref below.
Carole
Burrow, C., G. Young, and T. Senden. 2014: An antipodean Palaeospondylus? Paper presented at the 2014 Australian Earth Sciences Convention (AESC),
Sustainable Australia. Newcastle, NSW, July 7 - 10, 2014. Geological Society of Australia Abstracts volume 110: 119-120.

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Robert Bryson-Richardson
to me
Hi Ajay,
We used Drishti in a paper earlier this year.
The quail anatomy portal.
Ruparelia AA, Simkin JE, Salgado D, Newgreen DF, Martins GG, Bryson-Richardson RJ.
Database (Oxford). 2014 Apr 7;2014(0):bau028. doi: 10.1093/database/bau028. Print 2014.
(http://database.oxfordjournals.org/content/2014/bau028.full.pdf+html)

And the same data is also present on our website at quail.anatomyportal.org.

I am currently teaching at an EMBO imaging workshop - there will be lots of new drishti users in the next couple of days!

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Paul Bourke

Exhibitions
========
Pausiris, MONA (Museum of New and Old Art), Tasmania.
http://paulbourke.net/exhibition/MONA/
http://www.petermorse.com.au/2011/07/visualizing-pausiris-mona/

Fulldome volume visualisation piece
Played at SciTech (Perth) to 6 months
http://paulbourke.net/exhibition/mv2009/

iVEC visualisation Anthology features Toby Potters use of Drishti for visualising simulations of Supernova remnants
http://paulbourke.net/papers/artandscience.pdf


Papers
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Graphical exploration of the connectivity sets of alternated Julia sets; M, the set of disconnected alternated Julia sets. Nonlinear Dynamics, Springer, March 2013.
http://paulbourke.net/papers/Danca/


Web pages 2014
=============
Gauss Map tetrahedron 3D IFS
http://paulbourke.net/fractals/gaussmapifs/

Using Drishi file format for box counting work and using Drishi to check volumes
http://paulbourke.net/fractals/cubecount/

Used a presentation, including I've demonstration Volume Visualisation of Egyptian Mummies
http://paulbourke.net/papers/AESWA/

Pausiris and Drishti exampled here at BIT's 2nd Annual World Congress of Cultural & Creative IT Industries World EXPO Center, Dalian, China. Novel Image Capture and Presentation in Archaeology and Cultural Heritage
http://paulbourke.net/papers/cci2014/cci2014.pdf

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