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VolkerH / Lattice_Lightsheet_Deskew_Deconv

Open-source, GPU accelerated code for deskewing and deconvolving lattice light sheet data
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Support additional output formats Big Data Viewer, Imaris, .h5, Adaptive Particle Representation #8

Open VolkerH opened 5 years ago

VolkerH commented 5 years ago

Not urgent, but relatively easy to add output format options for Big Data Viewer and Imaris hdf5 via https://github.com/tlambert03/imarispy (should be easy).

Think about supporting adaptive particle representation as output to alleviate the storage problem https://github.com/AdaptiveParticles/LibAPR (no clue how difficult integration is, only heard about it yesterday).

VolkerH commented 5 years ago

Started experimenting with Adaptive Particle Representation.

Built a Docker container in which I have a python 3.5 instance with pyApr, scikit-image and ipython https://github.com/VolkerH/MyDockerStuff/tree/master/my_libapr

Using ipython I interactively converted a lattice stack (previously converted to np.uint8) to APR and did a reconstruction to tiff from the APR. These are the different file sizes:

-rwxr-xr-x 1 root root  6407198 Feb 14 14:27 my_apr_apr.h5
-rwxr-xr-x 1 root root 35391959 Feb 14 14:20 reconstructed.tif

However, pyApr seems to use a different ordering of dimensions internally, it seems that Z was swapped with something. Need to try reordering input and output array dimenstions and try again.

image

VolkerH commented 5 years ago

Also addresssing the data storage issue: https://git.embl.de/balazs/B3D