[SciPy-user] The IO library and image file formats -- compare with with PIL

Zachary Pincus zachary.pincus@yale....
Sun Jun 15 10:33:57 CDT 2008


Hi,

I've made little progress on this as I've been really quite busy with  
my research, I'm afraid. Sorry.

I will try to contact Fredrik today, though.

> I recently got more problems with reading a Zeiss Confocal Microscope
> (LSM) file -- as far as I can tell, LSM files are TIFF files, and
> ImageMagick recognizes the file in question as such ....

I recently have been looking at some numpy bindings for ImageMagick  
that were sent to me by an acquaintance at CMU. I can send them over  
(once I make sure there's no problem re-distributing them), if that  
would be helpful for anyone before we get a dependency-free solution.

Also on the microscopy-file-format question (a most vexed issue, to be  
sure), perhaps the tools at http://www.loci.wisc.edu/ome/formats.html  
will be useful. I've been using the bfconvert tool to turn Zeiss ZVI  
files into normal tiffs, and it handles a ton of other microscopy  
formats. (The bad news is that it's all in Java, so direct python  
bindings are rather unlikely.)

Zach



On Jun 15, 2008, at 3:00 AM, Sebastian Haase wrote:

> Zach et al,
>
> hi, has there been a development on this ... ?
> I.e. has anyone gotten in contact with Fredrik Lundh  ?
>
> I recently got more problems with reading a Zeiss Confocal Microscope
> (LSM) file -- as far as I can tell, LSM files are TIFF files, and
> ImageMagick recognizes the file in question as such ....
> The point here is,
> that I don't think that the Image-SIG mailing list is very  
> helpful ....
> (it'is only a fraction as good as what we are used to over here at
> SciPy ....  )
>
> So, (again,) it would be great if we could unite our image-io
> interests over here at SciPy...
>
> Thanks,
> Sebastian
>
>
>
> On Mon, Apr 21, 2008 at 10:49 PM, Robert Kern  
> <robert.kern@gmail.com> wrote:
>> On Mon, Apr 21, 2008 at 3:37 PM, Zachary Pincus <zachary.pincus@yale.edu 
>> > wrote:
>>> Let me look into whether this idea is at all feasible, and if it  
>>> is we
>>> can revisit the issue of whether it belongs anywhere near scipy.
>>> (Would getting Fredrik Lundh's OK to use various bits in this way  
>>> make
>>> things easier? He does seem much more responsive to direct queries
>>> than patch-submissions.)
>>
>> That would alleviate my concerns, yes.
>>
>> --
>> Robert Kern
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