A Python package relating to mouse brains (i.e., the 'ms' and 'brain' parts).

CURRENT:

• brainseries - functions for processing series of sparse brain slices. Specifically, in situ hybridisation images.
• atlas - dealing with atlas-related data
  • wrangle - manipulating data frames containing atlas related data and managing data in the file system.
  • visualise - plotting tools specific to anatomical data.
  • query - query the Allen Brain Institute's RMA API to obtain atlas-related data. Supports obtaining gridded gene expression data, Structure Unionize gene expression data, and raw insitu images. Plan to access GenePaint insitu images in the future.

OLD - LIGHTSHEET:

• io - reading and writing image data
• base - a number of fundemental functions that didn't fit elsewhere
• chain - several classes and functions for the serial processing of data using combinations of functions and specific arguments
• teraPrep - writing and nameing files according to TeraStitcher input requirments (for stitching lightsheet output)
• quantify - quantification of features (so far nuclear detection) in stitched light sheet data
  • processing - smaller fundemental processing functions
  • sample - applying processing pipelines to a directory of images sampled from a stitched lightsheet data set
  • volume - applying processing piplines to larger volumes
• map - mapping quantifications onto an atlas