array_gizmos

A collection of array operations and visualizations.

Installation

This module is in experimental/development mode and it also uses experimental dependancies.

Install the jp_doodle dependancy manually in development mode:

% git clone https://github.com/AaronWatters/jp_doodle.git
% cd jp_doodle
% pip install -e .
% cd ..

Install the H5Gizmos dependancy manually in development mode:

% git clone https://github.com/AaronWatters/H5Gizmos.git
% cd H5Gizmos
% pip install -e .
% cd ..

Then install this module in development mode:

% git clone https://github.com/AaronWatters/array_gizmos.git
% cd array_gizmos
% pip install -e .
% cd ..

How to use the labelled microscropy comparison visualization

This module includes a visualization implementation for comparing labelled structure volumes with microscopy volumes. The tool is designed for use with the blastoSPIM project data sets.

The notebooks/comparing labels and microscopy images.ipynb notebook demonstrates how to load volume arrays into the viewer and start the viewer in a notebook,

The bin/compare_npz_labels script demonstrates the how to load volume arrays into the viewer and start the viewer in a stand alone application.

The bin/compare_npz_labels script is installed with this module as a command line script which will open and display data from an numeric Python NPZ file formatted like the blastoSPIM project data sets. For example the following command opens the test data set:

% cd array_gizmos/notebooks/
% compare_npz_labels labels_and_image.npz 

Open gizmo using link (control-click / open link)

<a href="http://127.0.0.1:51303/gizmo/http/MGR_1663167750012_4/index.html" target="_blank">Click to open</a> <br> 
 GIZMO_LINK: http://127.0.0.1:51303/gizmo/http/MGR_1663167750012_4/index.html 

Open the link provided in a suitable web browser to start the visualization.

The volume alignment visualization

Follow this link for documentation on how to configure and use the label volume alignment interactive visualization.

Notes on the "overlayed segmentation" proof of concept (historical/deprecated)

Please follow this link for information on how to use the overlayed segmentation proof of concept. (Temporary link.)