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Dear all,
We (Seattle Children's, UW Friday Harbor Lab, and Duke) are recently funded=
by NSF to develop an add-on package for the open-source 3D Slicer for an i=
ntegrated experience to retrieve, process, digitize (i.e., landmark) and vi=
sualize 3D biological specimens. We are just kicking off the project, and e=
xpecting the first prototype to be ready by Spring 2019. Part of the projec=
t is to help the community to get their data into open-source formats. Ther=
e is no specific systematic focus, as long as image data are 3D. From our r=
esearch, we are well endorsed with vertebrate CT, microCT and surface scans=
from different scanner vendors, but are looking into sample data from dive=
rse set of organisms (and scales) to test our package. It will be greatly h=
elpful, if you can donate sample data for different organisms, and especial=
ly for 3D modalities apart from CT/microCT. There is a public data drop fol=
der located at:
https://faculty.washington.edu/maga/data_dropbox/
You will need to provide an e-mail address for us to get back in touch with=
you, in case we have a question. Also please do provide a brief descriptio=
n of the dataset. If you have multiple files (e.g., image stacks, associate=
d landmarks, segmentations, etc.), please zip them as a single file. If you=
send us any data in proprietary formats (Amira, Avizo, Geomagick, etc.), p=
lease provide us with a description of the format so that we can research w=
ays of converting them into an open format correctly and publish the workfl=
ow.
Feel free to forward this note to interested parties who may not be on morp=
hmet and thank you very much for your help!
M
A. Murat Maga, PhD
Asst. Professor
Division of Craniofacial Medicine
UW Dept. of Pediatrics
&
Member
Center for Developmental Biology and Regenerative Medicine
Seattle Children's Research Institute
--=20
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---=20
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To unsubscribe from this group and stop receiving emails from it, send an e=
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<p class=3D"MsoNormal">Dear all,<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">We (Seattle Children's, UW Friday Harbor Lab, and Du=
ke) are recently funded by NSF to develop an add-on package for the open-so=
urce 3D Slicer for an integrated experience to retrieve, process, digitize =
(i.e., landmark) and visualize 3D
biological specimens. We are just kicking off the project, and expecting t=
he first prototype to be ready by Spring 2019. Part of the project is to he=
lp the community to get their data into open-source formats. There is no sp=
ecific systematic focus, as long
as image data are 3D. From our research, we are well endorsed with vertebr=
ate CT, microCT and surface scans from different scanner vendors, but are l=
ooking into sample data from diverse set of organisms (and scales) to test =
our package. It will be greatly
helpful, if you can donate sample data for different organisms, and especi=
ally for 3D modalities apart from CT/microCT. There is a public data drop f=
older located at:<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal"><a href=3D"https://faculty.washington.edu/maga/data_=
dropbox/">https://faculty.washington.edu/maga/data_dropbox/</a>
<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">You will need to provide an e-mail address for us to=
get back in touch with you, in case we have a question. Also please do pro=
vide a brief description of the dataset. If you have multiple files (e.g., =
image stacks, associated landmarks,
segmentations, etc.), please zip them as a single file. If you send us any=
data in proprietary formats (Amira, Avizo, Geomagick, etc.), please provid=
e us with a description of the format so that we can research ways of conve=
rting them into an open format correctly
and publish the workflow. <o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">Feel free to forward this note to interested parties=
who may not be on morphmet and thank you very much for your help!<o:p></o:=
p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">M<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal">A. Murat Maga, PhD<o:p></o:p></p>
<p class=3D"MsoNormal">Asst. Professor<o:p></o:p></p>
<p class=3D"MsoNormal">Division of Craniofacial Medicine<o:p></o:p></p>
<p class=3D"MsoNormal">UW Dept. of Pediatrics<o:p></o:p></p>
<p class=3D"MsoNormal">&<o:p></o:p></p>
<p class=3D"MsoNormal">Member<o:p></o:p></p>
<p class=3D"MsoNormal">Center for Developmental Biology and Regenerative Me=
dicine<o:p></o:p></p>
<p class=3D"MsoNormal">Seattle Children's Research Institute<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
</div>
</body>
</html>
<p></p>
-- <br />
MORPHMET may be accessed via its webpage at <a href=3D"http://www.morphomet=
rics.org">http://www.morphometrics.org</a><br />
--- <br />
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