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add a bffile datasource and bioformats load path in image.py#1652

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barentine wants to merge 1 commit intopython-microscopy:masterfrom
barentine:bffile
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add a bffile datasource and bioformats load path in image.py#1652
barentine wants to merge 1 commit intopython-microscopy:masterfrom
barentine:bffile

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@barentine
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Addresses issue #bioformats installation. Posting as a draft for discussion - unclear if this is a direction we're interested in or not, but it was helpful for me to load some nd2 files from a collaborator.

Is this a bugfix or an enhancement?
enhancement
Proposed changes:

  • add option to load using bffile

loading tested with

  • single-channel nd2 file
  • multi-channel nd2 file

untested
-time series

  • other file types

@David-Baddeley
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Sounds good to me. Is installing bffile relatively painless? Is it painless enough that w might consider adding it to our dependencies?

@David-Baddeley
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I especially like the fact that it has a lazy loader (although the terminology is slightly misleading - asarray would usually imply forcing into memory ...)

@barentine barentine marked this pull request as ready for review March 12, 2026 17:02
@barentine
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Super painless to install over my recent 3.11 numpy 2.4 install via pip install bffile. If memory serves the install was fast, but the first time you call it from code it pulls java jars. Doesn't take long, but small oddity to note.
I think it would be pretty reasonable to add as a dependency.

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2 participants