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Parsing of whole-brain microscopy metadata

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micrometa

Reading of microscopy metadata

About

micrometa reads metadata from various whole-organ microscopes for use with BrainGlobe.

This is a work in progress, and currently the only metadata files supported are:

Parameters currently supported are:

  • Number of planes in the axial direction
  • Pixel sizes in x, y & z

To install

pip install micrometa

To use

from micrometa.micrometa import get_acquisition_metadata
metadata = get_acquisition_metadata("cellfinder_metadata.ini")
print(metadata.x_pixel_um)
print(metadata.y_pixel_um)
print(metadata.z_pixel_um)
print(metadata.num_planes)

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Parsing of whole-brain microscopy metadata

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