has anyone ever used ImageJ to read micro-CT scan data ?

[Maura Monville]

          Dear ImageJ experts,

We have just received a big file whose extension is ".isq" from a collaborator who does experiments on animals.
The file contains an unspecified number of micro-CT data acquired through a CT scanner,  used with small animals,
called Scanco Medical AG microCT40 or Scanco VivaCT40, Bruttisellen, Switzerland. The source spot size was 5 micro-meter  
at 45 KVp (with 0.5 mm Al filtering) sampling with 15x15x15 micro-meter voxels in a 30 mm diameter field
3 mm stacks of 200 sections at 2000 projections per revolution and an integration time of 300 milli-second per projection.

".isq" is a Scanco proprietary format.
We are looking for a s/w package capable of loading the micro-CT data and convert them into standard DICOM format.
We contacted Scanco technical support and were told the following "plugins for ImageJ may be found on the net",
which suggests that ImageJ, coupled with some appropriate plugin, can do the job.
No one in our group has ever used ImageJ. Therefore, I would greatly appreciate any comment and/or suggestion
helping us read the micro-CT data.
Thank you in advance.
       Kind regards,
              Maura Monville
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[José María Mateos]

2014-03-02 1:55 GMT+01:00 Maura Monville <[hidden email]>:
> ".isq" is a Scanco proprietary format.

Perhaps this plugin might be useful to you:
http://www.dent.med.uni-muenchen.de/~kkunzelm/exponent-0.96.3/index.php?section=49

Best,

José.

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[Michael Doube-4]

Hi Maura,

> We are looking for a s/w package capable of loading the micro-CT data and convert them into standard DICOM format.

BoneJ will open Scanco ISQ files for you, thanks to Karl-Heinz Kunzelmann's contribution of ISQ reader code. Just install BoneJ and drag-n-drop your ISQ file onto it, or run File > Import > Scanco ISQ

http://bonej.org/

As for saving as DICOM - I've found TIFF to be adequate as all the header information is kept.

Michael


<http://www.rvc.ac.uk>

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[Maura Monville]

Thank you very much to all of you for your valuable help.
I have a naive question. That is, shall I install ImageJ together with BoneJ ?
Or is BoneJ a self-contained package ?

Thank you again.
Regards,
maura

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Doube, Michael [[hidden email]]
Sent: Monday, March 03, 2014 11:48 AM
To: [hidden email]
Subject: Re: has anyone ever used ImageJ to read micro-CT scan data ?

Hi Maura,

> We are looking for a s/w package capable of loading the micro-CT data and convert them into standard DICOM format.

BoneJ will open Scanco ISQ files for you, thanks to Karl-Heinz Kunzelmann's contribution of ISQ reader code. Just install BoneJ and drag-n-drop your ISQ file onto it, or run File > Import > Scanco ISQ

http://bonej.org/

As for saving as DICOM - I've found TIFF to be adequate as all the header information is kept.

Michael


<http://www.rvc.ac.uk>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College.

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[Herbie-3]

Maura,

if you go, as recommended, to the BoneJ-Website you may find in the
first line:

"BoneJ is a plugin for bone image analysis in ImageJ."

Of course, a plugin needs the mother application, in this case, as
indicated, ImageJ.

HTH

Herbie

::::::::::::::::::::::::::::::::::::::::
On 04.03.14 05:49, Maura Monville wrote:

> Thank you very much to all of you for your valuable help.
> I have a naive question. That is, shall I install ImageJ together with BoneJ ?
> Or is BoneJ a self-contained package ?
>
> Thank you again.
> Regards,
> maura
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] On Behalf Of Doube, Michael [[hidden email]]
> Sent: Monday, March 03, 2014 11:48 AM
> To: [hidden email]
> Subject: Re: has anyone ever used ImageJ to read micro-CT scan data ?
>
> Hi Maura,
>
>> We are looking for a s/w package capable of loading the micro-CT data and convert them into standard DICOM format.
>
> BoneJ will open Scanco ISQ files for you, thanks to Karl-Heinz Kunzelmann's contribution of ISQ reader code. Just install BoneJ and drag-n-drop your ISQ file onto it, or run File > Import > Scanco ISQ
>
> http://bonej.org/
>
> As for saving as DICOM - I've found TIFF to be adequate as all the header information is kept.
>
> Michael
>
>
> <http://www.rvc.ac.uk>
>
> This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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