Login  Register

raw images

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
7 messages Options Options
Embed post
Permalink
Reply | Threaded
Open this post in threaded view
| More
Print post
Permalink

raw images

Lisa Dean
3 posts
Hi list users,

Could I have some help on the following problem please.

I have some DICOM images. I want to perform certain operations on them. My
program works better with raw images rather than DICOM so I converted these
DICOM series to a raw image using Image J.

I know that raw is just a string of binary. But, since the raw image I obtain
contains both the image and the header information from the DICOM  series,
I am confused as to how I may (i.e. how my program will) be able to distinguish
the image from the header, like, for eg:- how many bytes will be alloted to
the header and what all information will be present in the header(all the
information from the DICOM or only certain significant information?) and
also whether the header is followed by the image or vice-versa.

If I read the raw image using Image J's raw image reader I see that
the original
series is reproduced. How can I achieve this? Essentially I want to read in
the input raw image and separate the header and the image into 2 different
files.

Thanks a lot people
Lisa

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
| More
Print post
Permalink

loci with ndpi color

lartaud marc
7 posts
Hi list users,
I work with ndpi files from hamamatzu nanozoomer
I have problem with the new version of loci Bio format (4.4.4)
this is not  the right colors
the 4.4.2 version work correctely
Is it a bug in loci_tool.jar ?
thanks
marc lartaud

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
| More
Print post
Permalink

Re: raw images

James Ewing
23 posts
In reply to this post by Lisa Dean
Hi Lisa - I think the easiest way to get your result is to use one of the publicly available DICOM to Analyze filters.  Analyze files come with a separate header, and a raw data file, with .hdr and .img extensions, respectively.  Google "DICOM to Analyze" to get a little more information.

 - Jim

On Dec 7, 2012, at 1:23 AM, Lisa Dean wrote:

> Hi list users,
>
> Could I have some help on the following problem please.
>
> I have some DICOM images. I want to perform certain operations on them. My
> program works better with raw images rather than DICOM so I converted these
> DICOM series to a raw image using Image J.
>
> I know that raw is just a string of binary. But, since the raw image I obtain
> contains both the image and the header information from the DICOM  series,
> I am confused as to how I may (i.e. how my program will) be able to distinguish
> the image from the header, like, for eg:- how many bytes will be alloted to
> the header and what all information will be present in the header(all the
> information from the DICOM or only certain significant information?) and
> also whether the header is followed by the image or vice-versa.
>
> If I read the raw image using Image J's raw image reader I see that
> the original
> series is reproduced. How can I achieve this? Essentially I want to read in
> the input raw image and separate the header and the image into 2 different
> files.
>
> Thanks a lot people
> Lisa
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
| More
Print post
Permalink

Re: raw images

Richard VanMetter
27 posts
In reply to this post by Lisa Dean
Hi Lisa -

I think that ImageJ can easily provide the two files you would like to obtain from each DICOM file.

1. Open your DICOM image in ImageJ.
2. Save a raw data file as follows: select menu option ">File>Save As" and then select "Raw Data...". The raw image data from your DICOM image will be saved in a file with the same name, but with the extension ".raw". This DOES NOT include any of the header information, but only the pixel data.
3. Save the DICOM header as follows: select menu option ">Image>Show Info". This will open and "info" window that shows you all the DICOM header information along with some additional image information, like the number of bits per pixel, and the width, height and depth of your image file.
4. Select ">File>Save As" from the menu on the info window and save this information in a file (it will be an ascii text file readable in any text editor). The default file name for this text file is "Info-(image name).txt". You may change it if you wish.
5. Close all windows by selecting ">File>Close All" from the ImageJ menu.

If you have many images, you can automate this process by recording a macro. If you plan to work with images in the future, learning how to create ImageJ macros will be a useful skill. I would refer you to resources for learning the macro language on the ImageJ Developer Resources page "http://imagej.nih.gov/ij/developer/index.html". You can also get to this page from within ImageJ by selecting ">Help>Dev. Resources..." from the menu.

Richard VanMetter

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
| More
Print post
Permalink

Re: raw images

Lisa Dean
3 posts
Thank you Wayne, Richard. I didn't know about the part where information
can be saved as a text file. Definitely helpful. And thank you for the
additional detail Richard, it seems I'll have to create macros because I do
have a lot of images.

Yes Jim, I'd been starting to ponder that approach myself. However, I think
I'll first give a try to the raw images and text files, since information
in the text files can be read using any text editor unlike that of the .hdr
file. But, thank you for the input.


Lisa


On 8 December 2012 20:52, Richard VanMetter <[hidden email]> wrote:

> Hi Lisa -
>
> I think that ImageJ can easily provide the two files you would like to
> obtain from each DICOM file.
>
> 1. Open your DICOM image in ImageJ.
> 2. Save a raw data file as follows: select menu option ">File>Save As" and
> then select "Raw Data...". The raw image data from your DICOM image will be
> saved in a file with the same name, but with the extension ".raw". This
> DOES NOT include any of the header information, but only the pixel data.
> 3. Save the DICOM header as follows: select menu option ">Image>Show
> Info". This will open and "info" window that shows you all the DICOM header
> information along with some additional image information, like the number
> of bits per pixel, and the width, height and depth of your image file.
> 4. Select ">File>Save As" from the menu on the info window and save this
> information in a file (it will be an ascii text file readable in any text
> editor). The default file name for this text file is "Info-(image
> name).txt". You may change it if you wish.
> 5. Close all windows by selecting ">File>Close All" from the ImageJ menu.
>
> If you have many images, you can automate this process by recording a
> macro. If you plan to work with images in the future, learning how to
> create ImageJ macros will be a useful skill. I would refer you to resources
> for learning the macro language on the ImageJ Developer Resources page "
> http://imagej.nih.gov/ij/developer/index.html". You can also get to this
> page from within ImageJ by selecting ">Help>Dev. Resources..." from the
> menu.
>
> Richard VanMetter
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
| More
Print post
Permalink

Re: raw images

Mauro Maiorca
14 posts
Hi Lisa,

you might also consider the MetaIO file format, see
http://www.itk.org/Wiki/ITK/MetaIO/Documentation.
MetaIO files have a raw file and a header file (mhd) which can be
editable with any text editor. In ImageJ you can import/save MetaIO
files using this plugin:
http://www.kangli.org/code/MetaImage_Reader_Writer.html

The advantage of using MetaIO is that it is a widely recognized
format: you can read/write/process/convert MetaIO files using the gdcm
libraries, and many stand-alone programs including itk-snap, paraview,
slicer3d, etc. etc.

The major drawback of using MetaIO files instead of DICOMs is that you
might loose track of some information in the dicom header, for example
most of the patient's information. However, you definitely have most
of the info you might need for image processing/rendering, including
pixel spacing, pixel type, slice thickness, anatomical orientation,
etc etc.

cheers,
Mauro


On Mon, Dec 10, 2012 at 4:17 PM, Lisa Dean <[hidden email]> wrote:

> Thank you Wayne, Richard. I didn't know about the part where information
> can be saved as a text file. Definitely helpful. And thank you for the
> additional detail Richard, it seems I'll have to create macros because I do
> have a lot of images.
>
> Yes Jim, I'd been starting to ponder that approach myself. However, I think
> I'll first give a try to the raw images and text files, since information
> in the text files can be read using any text editor unlike that of the .hdr
> file. But, thank you for the input.
>
>
> Lisa
>
>
> On 8 December 2012 20:52, Richard VanMetter <[hidden email]> wrote:
>
>> Hi Lisa -
>>
>> I think that ImageJ can easily provide the two files you would like to
>> obtain from each DICOM file.
>>
>> 1. Open your DICOM image in ImageJ.
>> 2. Save a raw data file as follows: select menu option ">File>Save As" and
>> then select "Raw Data...". The raw image data from your DICOM image will be
>> saved in a file with the same name, but with the extension ".raw". This
>> DOES NOT include any of the header information, but only the pixel data.
>> 3. Save the DICOM header as follows: select menu option ">Image>Show
>> Info". This will open and "info" window that shows you all the DICOM header
>> information along with some additional image information, like the number
>> of bits per pixel, and the width, height and depth of your image file.
>> 4. Select ">File>Save As" from the menu on the info window and save this
>> information in a file (it will be an ascii text file readable in any text
>> editor). The default file name for this text file is "Info-(image
>> name).txt". You may change it if you wish.
>> 5. Close all windows by selecting ">File>Close All" from the ImageJ menu.
>>
>> If you have many images, you can automate this process by recording a
>> macro. If you plan to work with images in the future, learning how to
>> create ImageJ macros will be a useful skill. I would refer you to resources
>> for learning the macro language on the ImageJ Developer Resources page "
>> http://imagej.nih.gov/ij/developer/index.html". You can also get to this
>> page from within ImageJ by selecting ">Help>Dev. Resources..." from the
>> menu.
>>
>> Richard VanMetter
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
| More
Print post
Permalink

Re: loci with ndpi color

Melissa Linkert-2
123 posts
In reply to this post by lartaud marc
Hi Marc,

> I work with ndpi files from hamamatzu nanozoomer
> I have problem with the new version of loci Bio format (4.4.4)
> this is not  the right colors
> the 4.4.2 version work correctely
> Is it a bug in loci_tool.jar ?

The latest version of Bio-Formats is 4.4.5.  Do you see a problem with
that version as well?  If so, it would be very helpful if you could send
one .ndpi file that shows the problem, as well as listing the options
selected in the "Bio-Formats Import Options" window.

Regards,
-Melissa

On Fri, Dec 07, 2012 at 09:28:33AM +0100, lartaud marc wrote:

> Hi list users,
> I work with ndpi files from hamamatzu nanozoomer
> I have problem with the new version of loci Bio format (4.4.4)
> this is not  the right colors
> the 4.4.2 version work correctely
> Is it a bug in loci_tool.jar ?
> thanks
> marc lartaud
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html