Metadata-Version: 2.4
Name: spinosa
Version: 0.0.1
Summary: SPINOSA: structure- and probe-informed optophysiology of subcellular activity. The pipeline's first release is in preparation; this version holds the name and says what is coming.
Author-email: Wisam Reid <wisam@g.harvard.edu>
Project-URL: Repository, https://github.com/wisamreid/Dendritic_Imaging
Keywords: two-photon,calcium imaging,voltage imaging,glutamate imaging,dendrites,spines,optophysiology
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.8
Description-Content-Type: text/markdown

# SPINOSA

**SPINOSA** is an open-source analysis pipeline for optophysiology of dendrites: imaging the
activity of a single neuron's branches and spines, deep in living brain tissue, with calcium,
glutamate or voltage indicators under a scanning microscope.

It starts from two inputs a scientist already has: a hand-traced reconstruction of the neuron's
dendritic tree, and a structural image stack showing where that tree sits in depth. It registers
every frame of a movie to that structure, so the pipeline knows which branch each pixel belongs to
and how far the tissue has drifted up or down. From that it draws the regions, extracts a
fluorescence trace from each one, separates signal from the surrounding neuropil, and infers the
underlying spiking, using what is known about the indicator's own kinetics.

Every result is written with the evidence behind it: quality-control pictures, timing, and a record
of every setting, so a run can be checked file by file against another. It is built to be
reproducible, measured, and compatible with the tools the field already uses.

The name is Latin for "spiny"; *arbor spinosa* is the spiny tree.

## This release

Version 0.0.1 holds the name while the first release is prepared. It installs one command,
`spinosa`, which prints this description and where the pipeline is published.

The alias package `spinoza` installs this one, so a misspelled `pip install spinoza` still arrives here.
