Re: how integrate bioFormat with imagej

Posted by ctrueden on Sep 30, 2008; 2:14pm
URL: http://imagej.273.s1.nabble.com/how-integrate-bioFormat-with-imagej-tp3694911p3694914.html

Hi Prashant,

For information on using Bio-Formats to read in pixels as ImagePlus objects
(ImageJ's image construct), you should read the Bio-Formats ImageJ page:
http://www.loci.wisc.edu/ome/formats-imagej.html

And specifically, the linked ImageJ plugin code examples:
https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/utils/Read_Image.java
https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/utils/Mass_Importer.java

Once you are opening everything as ImagePlus objects, you can use the same
ImageJ-based processing techniques on both the compressed and uncompressed
data.

-Curtis

P. S. Your code looks fine except for the "MetaDataReader" object -- to my
knowledge that class is not part of ImageJ or Bio-Formats.

On Tue, Sep 30, 2008 at 12:28 AM, prashant <
[hidden email]> wrote:

> Thanks for your reply,
>
> It will be very grateful if you can give me some code example.
> I am using the following code for opening the compressed image from
> bioFormat.jar.
>
> String id = directory + name;
>
> ImageReader red = new ImageReader();
>
> red.setId(id);
>
> width = red.getSizeX();
>
> height = red.getSizeY();
>
> int num = noOfFrames = red.getImageCount();
>
> //for reading the metadata of image
>
> mdr = new MetaDataReader(red);
>
> bimg = new BufferedImage[num];
>
> for (int i = 0; i < num; i++)
>
> {
>
> bimg[i] = red.openImage(i);
>
> }
>
> red.close(true);
>
> It is giving me image in BufferedImage object form.
> thanks
>
>
>
>
>
>
> ----- Original Message ----- From: "Curtis Rueden" <[hidden email]>
> To: <[hidden email]>
> Sent: Monday, September 29, 2008 9:35 PM
> Subject: Re: how integrate bioFormat with imagej
>
>
>
>  Hi Prashant,
>>
>> Images opened using the Bio-Formats plugin should function the same as any
>> other images. You can process them with plugins and macros the same way.
>> The
>> only thing to watch out for is to avoid opening images as virtual stacks,
>> because while that option will save you a large amount of memory and is
>> good
>> for browsing, you will not be able to perform image manipulation
>> operations
>> unless you first convert to a normal stack using Image>Duplicate, as
>> described in this thread from the archive: <
>> https://list.nih.gov/cgi-bin/wa?A2=ind0809&L=imagej&H=1&P=15187>.
>>
>> -Curtis
>>
>> On Sun, Sep 28, 2008 at 11:46 PM, prashant <
>> [hidden email]> wrote:
>>
>>  Hi everyOne,
>>>
>>>         I am opening my multiframe compressed dicom image through
>>> bio-format.jar
>>>      and Uncompressed images through Imagej.jar.
>>>
>>>      I want to apply rotate,flip,invert option with images those are open
>>> with bio-Format.jar.
>>>      How can i integrate i.e. how can i perform such operation with
>>> images
>>> those are opened with bio-Format.jar.
>>>
>>>    It is same as when you open images in
>>> imagej--->plugIns---->LOCI---->bioFormat importer
>>>   Option.And you perform all operation with those image in Imagej.
>>>
>>> Thanks
>>>
>>> With Warm Regards
>>> --------------------------------------------------------------------
>>>
>>> Prashant Chandrakar
>>> Software Developer
>>> MedSynaptic Pvt Ltd
>>> 9270710943
>>> [hidden email]
>>>
>>> "If the facts don't fit the theory, change the facts."
>>>
>>>
>>