nd2 support
jim at rybarski.com
jim at rybarski.com
Mon Jul 21 22:23:24 EDT 2014
I'm looking for something that can directly read .nd2 files (an
undocumented Nikon format that seems to be similar to multipage TIFFs).
I've found
this: https://pythonhosted.org/SLOTH/_modules/sloth/read_nd2.html which
sorta works, though I'd like to clean it up and get it working in
scikit-image. But before I dive into that, I'd like to know:
1) Is there a better implementation somewhere, or does anyone have
experience parsing .nd2 files?
2) Since the format can contain hierarchical and multidimensional image
sets, would this require a new kind of abstraction for the io module? To
give a concrete example, the microscope data I'm working with contains 16
fields of view from different xy-positions on the sample slide, and in each
field of view there are three images for each time index (different
fluorescence filters). So while it would make sense to use io.MultiImage
for any given combination of field-of-view and filter, it wouldn't make
sense to do so for the entire nd2 file. I'm thinking perhaps there could be
some kind of intermediary object that allows you to drill down through the
hierarchy and at the end it returns a MultiImage object, or something like
that.
I'd appreciate any suggestions and I'd love to hear what everyone thinks.
Thanks!
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