Hi,
nd2reader is having trouble reading a file as it finds "Zs" that are not there.
Image was acquired with triggered imaging
1 Z, 120T, 2044 Y, 2048 X, 24 Visit Points.
pims_nd2readerSDK and pims.bioformats read the file fine.
I can share but this file is 20GB.
It did this to 2 files from two different experiments.
I'll try to crop the data to a small XY, if it replicates I'll share.
%matplotlib inline
import pims
from nd2reader import ND2Reader
from pims import ND2_Reader as nd2_sdk
# fname = 'igfp1_caruby5_continue001trigger003.nd2'
fname = '../Data/igfp1_caruby5_VOG002.nd2'
# fname = 'igfp3_caruby3_rutin_bvd_f2_2days_xy02.nd2'
# fname = '/tmp/test.ome.tiff'
frames = ND2Reader(fname)
frames_sdk = nd2_sdk(fname)
frames_bioformats = pims.bioformats.BioformatsReader(fname)
# frames.iter_axes = 't' # 't' is the default already.
# frames.bundle_axes = 'zyx' # when 'z' is available, this will be default
print(frames.sizes)
print(frames_sdk.sizes)
print(frames_bioformats.sizes)
{'x': 2048, 'y': 2044, 'c': 2, 't': 51, 'z': 1224, 'v': 24}
{'x': 2048, 'y': 2044, 'c': 2, 't': 51, 'm': 24}
{'x': 2048, 'y': 2044, 'c': 2, 't': 51}
Hi,
nd2reader is having trouble reading a file as it finds "Zs" that are not there.
Image was acquired with triggered imaging
1 Z, 120T, 2044 Y, 2048 X, 24 Visit Points.
pims_nd2readerSDK and pims.bioformats read the file fine.
I can share but this file is 20GB.
It did this to 2 files from two different experiments.
I'll try to crop the data to a small XY, if it replicates I'll share.