Covert stack of 2-D images into a 3-D volume

[Seetha S]

Hi,

I have a stack of 2-D images from x-ray computed tomography that I would
like to convert into a 3-D volume so I can do an average bulk porosity
analysis using BoneJ..can anyone please let me know how I construct the
volume using ImageJ?

Thank you.

--
Seetha

[Seetha S]

Hi,

I am reposting this question to ask if anyone could help me with
constructing a 3-D volume from a stack of 2-D computed tomography images
using ImageJ. I tried File > Import > Image Sequence as instructed in the
software manual but it did not allow me to select more than one image at a
time and I couldn't figure out how else to do it.

Any help that anyone can provide me in this regard would be greatly
appreciated.

Thank you in advance!

---------- Forwarded message ----------
From: Seetha S <[hidden email]>
Date: Thu, May 5, 2011 at 12:03 PM
Subject: Covert stack of 2-D images into a 3-D volume
To: IMAGEJ <[hidden email]>


Hi,

I have a stack of 2-D images from x-ray computed tomography that I would
like to convert into a 3-D volume so I can do an average bulk porosity
analysis using BoneJ..can anyone please let me know how I construct the
volume using ImageJ?

Thank you.

--
Seetha



--
Seetha

[Mats Leif Moskopp]

hello,

so you have a 2d stack and you want to have a volume, am i right?
i would propose:
Plugins -> 3D -> ImageJ 3D Viewer

i hope it helped
greetings
mats moskopp

2011/5/16 Seetha S <[hidden email]>

> Hi,
>
> I am reposting this question to ask if anyone could help me with
> constructing a 3-D volume from a stack of 2-D computed tomography images
> using ImageJ. I tried File > Import > Image Sequence as instructed in the
> software manual but it did not allow me to select more than one image at a
> time and I couldn't figure out how else to do it.
>
> Any help that anyone can provide me in this regard would be greatly
> appreciated.
>
> Thank you in advance!
>
> ---------- Forwarded message ----------
> From: Seetha S <[hidden email]>
> Date: Thu, May 5, 2011 at 12:03 PM
> Subject: Covert stack of 2-D images into a 3-D volume
> To: IMAGEJ <[hidden email]>
>
>
> Hi,
>
> I have a stack of 2-D images from x-ray computed tomography that I would
> like to convert into a 3-D volume so I can do an average bulk porosity
> analysis using BoneJ..can anyone please let me know how I construct the
> volume using ImageJ?
>
> Thank you.
>
> --
> Seetha
>
>
>
> --
> Seetha
>

[Albert Cardona-2]

2011/5/16 Seetha S <[hidden email]>:

> Hi,
>
> I am reposting this question to ask if anyone could help me with
> constructing a 3-D volume from a stack of 2-D computed tomography images
> using ImageJ. I tried File > Import > Image Sequence as instructed in the
> software manual but it did not allow me to select more than one image at a
> time and I couldn't figure out how else to do it.
>
> Any help that anyone can provide me in this regard would be greatly
> appreciated.
>
> Thank you in advance!

If the images exist as a list of files, one image per file, in a
folder, then choose "File - Import - Image Sequence", or drag and drop
the folder to the ImageJ toolbar.

Albert

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/

[Seetha S]

Hi,

Thank you all for your responses. I was able to successfully construct a 3-D
volume from in ImageJ. I then loaded it into the Image 3D viewer to view the
3D volume but when I tried to estimate the porosity of this volume using the
BoneJ plugin I received an error message saying that I needed a binary,
8-bit or 16-bit image to calculate the volume fraction. I am unsure how to
correctly binarise my image by applying thresholds. Could anyone please help
me in this regard?

Thank you all, for your time and help!

On Mon, May 16, 2011 at 3:30 PM, Mats Leif Moskopp
<[hidden email]>wrote:

> hello,
>
> so you have a 2d stack and you want to have a volume, am i right?
> i would propose:
> Plugins -> 3D -> ImageJ 3D Viewer
>
> i hope it helped
> greetings
> mats moskopp
>
> 2011/5/16 Seetha S <[hidden email]>
>
> > Hi,
> >
> > I am reposting this question to ask if anyone could help me with
> > constructing a 3-D volume from a stack of 2-D computed tomography images
> > using ImageJ. I tried File > Import > Image Sequence as instructed in the
> > software manual but it did not allow me to select more than one image at
> a
> > time and I couldn't figure out how else to do it.
> >
> > Any help that anyone can provide me in this regard would be greatly
> > appreciated.
> >
> > Thank you in advance!
> >
> > ---------- Forwarded message ----------
> > From: Seetha S <[hidden email]>
> > Date: Thu, May 5, 2011 at 12:03 PM
> > Subject: Covert stack of 2-D images into a 3-D volume
> > To: IMAGEJ <[hidden email]>
> >
> >
> > Hi,
> >
> > I have a stack of 2-D images from x-ray computed tomography that I would
> > like to convert into a 3-D volume so I can do an average bulk porosity
> > analysis using BoneJ..can anyone please let me know how I construct the
> > volume using ImageJ?
> >
> > Thank you.
> >
> > --
> > Seetha
> >
> >
> >
> > --
> > Seetha
> >
>

--
Seetha

[John Oreopoulos]

Seetha,

See this section of the ImageJ documentation guide:

http://rsbweb.nih.gov/ij/docs/guide/userguide-26.html#toc-Subsection-26.8

as well as this section regarding image type conversion:

http://rsbweb.nih.gov/ij/docs/guide/userguide-25.html#toc-Subsection-25.1


Best,

John Oreopoulos
Research Assistant
Spectral Applied Research
Richmond Hill, Ontario
Canada
www.spectral.ca


On 2011-05-17, at 9:24 AM, Seetha S wrote:

> Hi,
>
> Thank you all for your responses. I was able to successfully construct a 3-D
> volume from in ImageJ. I then loaded it into the Image 3D viewer to view the
> 3D volume but when I tried to estimate the porosity of this volume using the
> BoneJ plugin I received an error message saying that I needed a binary,
> 8-bit or 16-bit image to calculate the volume fraction. I am unsure how to
> correctly binarise my image by applying thresholds. Could anyone please help
> me in this regard?
>
> Thank you all, for your time and help!
>
> On Mon, May 16, 2011 at 3:30 PM, Mats Leif Moskopp
> <[hidden email]>wrote:
>
>> hello,
>>
>> so you have a 2d stack and you want to have a volume, am i right?
>> i would propose:
>> Plugins -> 3D -> ImageJ 3D Viewer
>>
>> i hope it helped
>> greetings
>> mats moskopp
>>
>> 2011/5/16 Seetha S <[hidden email]>
>>
>>> Hi,
>>>
>>> I am reposting this question to ask if anyone could help me with
>>> constructing a 3-D volume from a stack of 2-D computed tomography images
>>> using ImageJ. I tried File > Import > Image Sequence as instructed in the
>>> software manual but it did not allow me to select more than one image at
>> a
>>> time and I couldn't figure out how else to do it.
>>>
>>> Any help that anyone can provide me in this regard would be greatly
>>> appreciated.
>>>
>>> Thank you in advance!
>>>
>>> ---------- Forwarded message ----------
>>> From: Seetha S <[hidden email]>
>>> Date: Thu, May 5, 2011 at 12:03 PM
>>> Subject: Covert stack of 2-D images into a 3-D volume
>>> To: IMAGEJ <[hidden email]>
>>>
>>>
>>> Hi,
>>>
>>> I have a stack of 2-D images from x-ray computed tomography that I would
>>> like to convert into a 3-D volume so I can do an average bulk porosity
>>> analysis using BoneJ..can anyone please let me know how I construct the
>>> volume using ImageJ?
>>>
>>> Thank you.
>>>
>>> --
>>> Seetha
>>>
>>>
>>>
>>> --
>>> Seetha
>>>
>>
>
>
>
> --
> Seetha