Re: Error when building from git
Hi Guillaume, Sorry for the trouble with the FreeImage loading -- I'm glad you got it straightened out. As Stéfan mentioned, we're trying to get this a lot smoother, and it should be soon! Please let me know if you have any other problems with FreeImage. I should also mention (as you're doing microscopy and may need to get at image metadata from time to time, as I do) that I recently added that capability to the freeimage wrappers. See e.g.: https://github.com/scikits-image/scikits-image/blob/master/skimage/io/_plugi...
Also, I just ran into another problem with freeimage... [...]
After some investigation, I found that I had to link /usr/lib/ libfreeimage.so.3 with /usr/lib/libfreeimage.so to pass the plugin test:
I just discovered this myself earlier this week. Zachary Pincus has been working on better library location (on Windows mainly), so we should have that sorted out soon. Would you mind creating an issue on GitHub in the mean time, so that we don't lose track of it?
https://github.com/scikits-image/scikits-image/pull/134 This should fix the above problem and a host of others. A mechanism for auto-downloading a freeimage library on Win/Mac is still in progress... I'm not sure how to best integrate that with the distutils, but here's what I have for a start: https://github.com/zachrahan/scikits-image/tree/freeimage-install-libs https://github.com/zachrahan/freeimage-sharedlib Zach
Hi Zachary 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? Guillaume Le 10/02/2012 15:21, Zachary Pincus a écrit :
Hi Guillaume,
Sorry for the trouble with the FreeImage loading -- I'm glad you got it straightened out. As Stéfan mentioned, we're trying to get this a lot smoother, and it should be soon! Please let me know if you have any other problems with FreeImage.
I should also mention (as you're doing microscopy and may need to get at image metadata from time to time, as I do) that I recently added that capability to the freeimage wrappers. See e.g.: https://github.com/scikits-image/scikits-image/blob/master/skimage/io/_plugi...
Also, I just ran into another problem with freeimage... [...] After some investigation, I found that I had to link /usr/lib/ libfreeimage.so.3 with /usr/lib/libfreeimage.so to pass the plugin test: I just discovered this myself earlier this week. Zachary Pincus has been working on better library location (on Windows mainly), so we should have that sorted out soon. Would you mind creating an issue on GitHub in the mean time, so that we don't lose track of it?
https://github.com/scikits-image/scikits-image/pull/134
This should fix the above problem and a host of others.
A mechanism for auto-downloading a freeimage library on Win/Mac is still in progress... I'm not sure how to best integrate that with the distutils, but here's what I have for a start: https://github.com/zachrahan/scikits-image/tree/freeimage-install-libs https://github.com/zachrahan/freeimage-sharedlib
Zach
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
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
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
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?
I'll make a PR for the tifffile / scikits-plugin integration shortly. As far as BioFormats and python/java, I think Ray has had the most experience working with this, if he wants to weigh in on that. Zach
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
participants (3)
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Christoph Gohlke
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Guillaume Gay
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Zachary Pincus