channel-z ordering problem when reading lif

[SeanLeRoy]

See the original issue here from aicsimageio. In short there is a bug in the third-party LIF reader this package uses (readlif) with some LIF files saved by the LAS X Navigator.

Originally submitted by @TomPJWyatt

[maxshcherbina]

Heart breaking issue here - hope Arcadia-Science (the new readlif owners) can fix this problem, as they do seem to be aware of it!

https://github.com/Arcadia-Science/readlif/blob/master/readlif/reader.py#L189

I'll post the error so that others can find this easier later: Atypical imaging experiment, please use get_plane() instead of get_frame()

[imagejan]

On the readlif side, this is fixed with Arcadia-Science/readlif#52 but not yet released.

[toloudis]

Great to hear. I wonder if they plan to do a versioned release. Also wonder if we can test by getting the dependency from github source

[imagejan]

if we can test by getting the dependency from github source

I opened #18 to test with the latest readlif from GitHub source.

(I first had to set channel_as_second_dim manually to make the (some) tests fail with readlif-0.6.4, before testing that it is fixed with the latest source version.)