http://imagej.273.s1.nabble.com/how-integrate-bioFormat-with-imagej-tp3694911p3694916.html
the Util.openProcessors(IFormatReader, int) method. This is very basic -- I
suggest you study up on your Java. If you are receiving an error, it is
questions specifically about ImageJ, such as the ImageJ API. For questions
> Thanks for your reply,
>
> I saw you example.But i have a problem.
> In example they uses
>
> IFormatReader r = new ChannelSeparator();
>
> But for opening my Images i am using following code.
>
> ImageReader red = new ImageReader();
>
> So how can i create stack with these object.
>
> When i pass Object red to Util.openProcessor() method
>
> it is giving me error.
>
> Because it takes IFormatReader object as parameter.
>
> So what can i do,Please help me
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ----- Original Message ----- From: "Curtis Rueden" <
[hidden email]>
> To: <
[hidden email]>
> Sent: Tuesday, September 30, 2008 7:44 PM
>
> Subject: Re: how integrate bioFormat with imagej
>
>
> 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."
>>>>>
>>>>>
>>>>>
>>>>
>>