wrong number of z plane / time points

[jboulanger]

Hello,
I might be missing something but a file with 1419 images planes as a 2D time sequence is decoded as an image with 1419 z planes and 1419 time points.

from nd2reader import ND2Reader

with ND2Reader('../data/example.nd2') as images:
  print('Image size:', images.sizes)
  print("Number of images: ", len(images))

gives:

Image size: {'x': 512, 'y': 512, 't': 1419, 'z': 1419}
Number of images: 1419

The iter axe is also misidentify as being z instead of t..

from nd2reader import ND2Reader

with ND2Reader('../data/example.nd2') as images:
    images.iter_axes = 'z' # instead  of 't'
    plt.imshow(images[3])

[rbnvrw]

Thank you for your report @jboulanger. The iter_axes attribute is something you can change yourself to determine over which axes to iterate, see this documentation: http://soft-matter.github.io/pims/v0.5/multidimensional.html

The size issue is a bit more challenging. Can you post a screenshot of what it is supposed to be in the ND2 software?

[jboulanger]

Thank you for looking into this.

I agree it is possible to change the iter_axes but still one would expect to have to use 't' for a time sequence and 'z' for a 3D image stack.

Here are screenshot of the image window in NIS Elements:

And here is the field in 'Description' field of the image properties:

Metadata:
Dimensions: T(1419)
Camera Name: Flash4.0, SN:100266
Numerical Aperture: 0.75
Refractive Index: 1
Name: DIC Camera
Component Count: 1
Modality: Brightfield
Camera Settings: Exposure: 3 ms
Binning: 1x1
Scan Mode: Fast
Microscope Settings: Microscope: Ti2 Microscope
DIC Prism, position: In
Bertrand Lens, position: Out
Nikon Ti2, FilterChanger(Turret-Lo): 1 (GFP-L)
Nikon Ti2, Shutter(FL-Lo): Opened
Nikon Ti2, Shutter(DIA LED): Active
Nikon Ti2, Illuminator(DIA): On
Nikon Ti2, Illuminator(DIA) Iris intensity: 84.2
LightPath: L100
Analyzer Slider: Extracted
PFS, state: Off
PFS, offset: 8838
PFS, mirror: Inserted
PFS, Dish Type: Glass
Zoom: 1.50x
Sutter Lambda 10-3, FilterChanger(Filter C): 8 (Analyser)
Sutter Lambda 10-3, Shutter(DIA): Opened
Sutter Lambda 10-3, Shutter(DIA) mode: Fast
Spectra/AuraII, Shutter(NIJI): Closed
Spectra/AuraII, MultiLaser(Spectra):
Line:1; ExW:395; Power: 25.0; Off
Line:2; ExW:445; Power: 10.0; Off
Line:3; ExW:470; Power: 14.0; Off
Line:4; ExW:510; Power: 12.0; Off
Line:5; ExW:550; Power: 10.0; Off
Line:6; ExW:635; Power: 10.0; Off

Time Loop: 1419

• Equidistant (Duration 5 s)