[Insight-users] Reading LSM images

Luis Ibanez luis.ibanez at kitware.com
Mon Feb 15 17:47:54 EST 2010 

Hi Alex,

Thanks for the reminder.


Jesse:

You may want to look at bioimageXD
if you don't mind using GPL code:
http://www.bioimagexd.net/index.php?option=com_content&task=view&id=14&Itemid=28


Otherwise,
you probably could use the vtkLSMReader
in gofigure2, that is under a BSD license,
as Alex pointed out.



    Regards,


           Luis


-------------------------------------------------------
On Mon, Feb 15, 2010 at 11:46 AM, Alexandre GOUAILLARD
<agouaillard at gmail.com> wrote:
> hi luis, dan, all,
>
> luis, you might not remember that long thread we had about LSM reader,
> but the ITK one does not handle multi channels.
>
> Dan (and other from bioimageXD) made their vtkLSM reader available
> under BSD, and that s the one we eventually used for GoFigure. That
> the one gaethan is also using on a daily basis.
>
> As dan pointed out, the best reader, or the one including most
> functionaity and the most up to date, out there might be the one from
> OME, and curtis should have a wrapping between OME and ITK IO working
> (in cc).
>
> good luck.
>
> alex.
>
> On Sun, Feb 14, 2010 at 5:21 AM, Jesse Stokum <jessestokum at gmail.com> wrote:
>> Luis,
>>
>> I've surrounded my reader->update() line with a try, catch block that
>> catches itk::ExceptionObject. It doesn't seem to be even getting to
>> the catch block- simple std::cout statements inside the catch block
>> are not showing. The following unhandled exception appears however
>> when I run my program on the vs debugger:
>>
>> The thread 'Win32 Thread' (0x1a7c) has exited with code 0 (0x0).
>> Unhandled exception at 0x00b0a890 in CellSegment.exe: 0xC0000005:
>> Access violation writing location 0x08fc0040.
>>
>> The breakpoint that is detected by vs is in line 1116 of the class
>> itkTIFFImageIO.cxx.
>>
>> Thanks,
>>
>> Jesse
>>
>>
>>
>> On Sat, Feb 13, 2010 at 3:38 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>> Hi Jesse,
>>>
>>> Thanks for the clarification.
>>>
>>> You are right, if the 3D image is in a single file, then
>>> using the ImageFileReader is the correct way to
>>> proceed.
>>>
>>> Could you please post to the list the exact text
>>> that you get from the Exceptions ?
>>>
>>> If you need examples on how to catch exceptions
>>> and print their error messages, you will find many
>>> of them in the directories under
>>>
>>>                     Insight/Examples
>>>
>>>
>>>     Thanks
>>>
>>>
>>>             Luis
>>>
>>>
>>> -----------------------------------------------------------------
>>> On Sat, Feb 13, 2010 at 12:33 PM, Jesse Stokum <jessestokum at gmail.com> wrote:
>>>> Luis,
>>>>
>>>> Thanks for the quick reply, I really appreciate it. The lsm image
>>>> stack that I'm working with are actually all in a single file - which
>>>> is why I hesitated to use the ImageSeriesReader for this one. I
>>>> suppose I could always split the stack into a series of slices imagej
>>>> or something else, but it would be more time efficient to just read in
>>>> the entire file. Also, intuitively I think that I would get better
>>>> filtering results if I handled it as a 3d image, though I could be
>>>> wrong about that. Thanks!
>>>>
>>>> Jesse
>>>>
>>>> On Fri, Feb 12, 2010 at 5:07 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>>>> Hi Jesse,
>>>>>
>>>>>
>>>>> If you have the images in independent files (one file per slice),
>>>>> you should use the itk::ImageSeriesReader (instead of the
>>>>> itk::ImageFileReader).
>>>>>
>>>>>
>>>>> The LSM reader in ITK should be able to manage three channels
>>>>> (three components per pixel).
>>>>>
>>>>> You will find examples on how to use the ImageSeriesReader
>>>>> in the ITK Software Guide
>>>>>
>>>>>                   http://www.itk.org/ItkSoftwareGuide.pdf
>>>>>
>>>>> in the chapter "Reading and Writing Images",
>>>>>
>>>>> and you will find source code examples in the directory:
>>>>>
>>>>>                           Insight/Examples/IO
>>>>>
>>>>> in particular, you may find interesting the example:
>>>>>
>>>>>            RGBImageSeriesReadWrite.cxx
>>>>>
>>>>> you probably only need to replace there the PNGImageIO
>>>>> class with a LSMImageIO class.
>>>>>
>>>>>
>>>>> Please give it a try and let us know if you find any problems.
>>>>>
>>>>> BTW: I you get any Exceptions, please post to the list
>>>>> the *exact* error message that you get from the exception.
>>>>>
>>>>>
>>>>>     Thanks
>>>>>
>>>>>
>>>>>
>>>>>           Luis
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------------------------
>>>>> On Fri, Feb 12, 2010 at 12:34 PM, Jesse Stokum <jessestokum at gmail.com> wrote:
>>>>>> I'm trying to use ITK's ImageFileReader to read in LSM format images
>>>>>> and my code is abruptly throwing exceptions. The images are three
>>>>>> channel, and are ~30 slices. Should I consider them 3d images? Here's
>>>>>> the code in my main() I've been trying:
>>>>>>
>>>>>>        typedef itk::RGBPixel<unsigned char> PixelType;
>>>>>>        typedef itk::Image<PixelType, 3> ImageType;
>>>>>>
>>>>>>        typedef itk::ImageFileReader<ImageType> ReaderType;
>>>>>>        typedef itk::LSMImageIO ImageIOType;
>>>>>>        typedef itk::ImageFileWriter<ImageType> WriterType;
>>>>>>
>>>>>>        ReaderType::Pointer reader = ReaderType::New();
>>>>>>        ImageIOType::Pointer lsmImageIO = ImageIOType::New();
>>>>>>        reader->SetImageIO(lsmImageIO);
>>>>>>        reader->SetFileName("Tests.lsm");
>>>>>>
>>>>>> Are lsm pixels vector pixels? I guess I'm just unsure how to handle
>>>>>> this situation. Thanks in advance!
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