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

Sebastian Haase haase@msg.ucsf....
Sun Jun 15 11:50:18 CDT 2008


On Sun, Jun 15, 2008 at 5:33 PM, Zachary Pincus <zachary.pincus@yale.edu> wrote:
> 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.
>
great - thanks.

>> 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.
>
What I have seen of imagemagick in terms of binding was very discouraging ....
( Mostly abandoned stuff because I.M. seems to be moving a target;
with every release a new API -- maybe that has changed by now. ) Main
point though: PIL is really close to what we need....

> 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.)

Yeah I know about this. I actually tried some Jython on it: and I made
a nice script which converts "whole directory trees full of "
LOCI-readable files into my preferred (memory mappable) file format
(it's close to the Deltavision format, a derivative of the MRC format)

- Sebastian

>
> 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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