mapzebrain-viewer

Graphical user interface for viewing markers and regions of the MapZeBrain atlas - for quick and simple visualization of ROI locations against the atlas data in Python. This viewer uses the provided MapZeBrain API, but is not affiliated with the project in any way.

It enables the export of anatomical images for different views, while using matplotlib for keeping with the style of other publication figures:

Installation

Run pip install git+https://github.com/thladnik/mapzebrain-viewer in your Python environment.

In order to enable exports of pretty matplotlib renderings of the data, either run pip install matplotlib or install mapzebview with optional dependencies pip install git+https://github.com/thladnik/mapzebrain-viewer[pretty]

Usage

Simple

Either run it from the command line useing the mapzebview command or start it from within your Python code:

import mapzebview

mapzebview.run()

By default the interface uses the jf5Tg line. This behavior can be changed by changing the variable mapzebview.config.default_marker_name: str

Advanced

To use a different marker line:

import mapzebview

mapzebview.run(marker='mpn212Tg')

To pre-select regions (can also be toggled in UI):

import mapzebview

mapzebview.run(regions=['pretectum', 'periventricular layer', 'oculomotor nucleus'])

To directly plot ROI locations from within the analysis:

import mapzebview

# Option 1
import pandas as pd
roi_coordinates = pd.read_hdf('path/to/file.hdf5')

# Option 2
import numpy as np
roi_coordinates = np.load('path/to/file.npy')

mapzebview.run(rois=roi_coordinates)  # pandas.DataFrame with x/y/z columns or numpy.ndarray with shape Nx3

To plot ROI locations from a file directly, .hdf5 or .npy files can also be dropped into the interface

To plot multiple sets of ROIs at once:

import mapzebview

import pandas as pd
import numpy as np

roi_sets = {
    'ROI set 1': pd.read_hdf('path/to/file.hdf5'), 
    'ROI set 2': np.load('path/to/file.npy'), 
    'Some other set': np.load('path/to/other/file.npy')
}

mapzebview.run(rois=roi_sets)  # dictionary containing pairs of name: pandas.DataFrame/numpy.ndarray