micrometa

Reading of microscopy metadata

About

micrometa reads metadata from various whole-organ microscopes for use with cellfinder and amap.

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

• BakingTray recipe files
• mesoSPIM metadata files
• amap custom metadata files
• cellfinder custom metadata files

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)