test aics internal nd2 files

[toloudis]

Use Case

We would like to do some early testing to make sure our nd2 reader can handle some of the data we are recently generating:

From Derek:
\\aics.vast01.corp.alleninstitute.org\aics\playground\NikonLongTimelapse

From Antoine:
\\allen\aics\microscopy\Data\RnD_Sandbox\Nikon_2DMIP_LongTimelapse

Solution

Run something like this and report results.. mostly ensure no crashes.

img = AICSImage(path, reader=ND2Reader)
print(img.shape)
print(img.dims)
print(img.channel_names)
print(img.physical_pixel_sizes)
testdata = img.get_image_data("YX", Z=z, T=t, C=c)
print(testdata.dtype)
# display data
...

[toloudis]

also can test BioformatsReader as a fallback in case ND2Reader can't handle it.

[toloudis]

From Caroline:
here’s a folder of our imaging from our nikon demo - so many .nd2 files to choose from! //allen/aics/microscopy/Jie/Microscope demo/NIkon W1 onsite demo Feb 2023
here’s a specific file that I know has multiple channels, z planes, and timepoints…
//allen/aics/microscopy/Jie/Microscope demo/NIkon W1 onsite demo Feb 2023/Caroline/20230223_carolineTL003-sandwich.nd2

[SeanLeRoy]

Caroline and Derek's file were able to be read with the reader at this commit. Antoine's files aren't ND2 files so they didn't work. Closing this unless there is more we can do to test.