Tifffile.py as a plugin vs BioFormats

[Guillaume Gay]

Hi,

Thank you Christoph for the suggestion, I think I will use your 
solution, which works fine for me.


Of course BioFormats is kind of the golden standard for those microscopy 
formats but I don't feel very comfortable with the java/python bindings 
(isn't it adding a java dependency, and making platform changes more 
complex?).



Guillaume



Le 10/02/2012 22:20, Christoph Gohlke a écrit :
> On 2/10/2012 7:46 AM, Zachary Pincus wrote:
>>> Indeed metadata are important, thanks for pointing this out, I'll 
>>> have a look at it (though I find metamorph is not so good at 
>>> recording good metadata).
>>>
>>> By the way, I have both .stk and .tif images, so I use Christoph 
>>> Gohlke tifffile.py for the .stk files. Is ther any chance this will 
>>> be integrated to skimage?
>>
>> Wow! Somehow I was not familiar with Christoph's tifffile.py... 
>> that'll be very handy for these cursed LSM files I have laying 
>> around. (No help for the ZVIs, but I already have a silly 
>> zvi->ome-tiff workflow for them.)
>>
>> Perhaps Christoph, who frequents this list, can weight in on whether 
>> it would be a good idea to wrap this in as a skimage IO plugin, or if 
>> it's best as a separate project...
>>
>> Zach
>
> A skimage io plugin for tifffile.py is straightforward (attached). The 
> module already implements imread, imsave, and imshow functions. Those 
> functions return/save/show n-dimensional numpy arrays (n>=2). I'm not 
> sure skimage can handle n>3?
>
> Tifffile.py and tifffile.c are BSD licensed, so it is no problem to 
> include them with skimage. I don't think the module itself should be 
> maintained or supported as part of skimage.
>
>
> Regarding those cursed, broken, undocumented or NDAed, microscopy file 
> formats:
>
> I'm aware of two other projects that strive to read LSM files: 
> pylibtiff <http://code.google.com/p/pylibtiff/> and pylsm 
> <http://www.freesbi.ch/pylsm>.
>
> How about a plugin for BioFormats 
> <http://loci.wisc.edu/software/bio-formats>, which supports many more 
> formats? The Cellprofiler project contains GPLed bindings 
> <https://svn.broadinstitute.org/CellProfiler/trunk/CellProfiler/bioformats/>.
>
> Christoph
>
>
>

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