[Insight-users] Reading LSM images

Thu Feb 18 04:17:10 EST 2010

Hi All,

On Mon, 15 Feb 2010, Luis Ibanez wrote:

> 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

Actually the license of LSM reader was changed to be BSD license some time 
ago to make it easier for others (like gofigure2) to use it.

Regards,
Lassi

> 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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>>>>>>
>>>>>
>>>>
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-- 
Lassi Paavolainen, M.Sc
Software Engineer, PhD Student in Computer Science
BioImageXD (http://www.bioimagexd.net)
University of Jyväskylä
lassi.paavolainen at jyu.fi