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https://github.com/aaronwatters/array_gizmos
A collection of array operations and visualizations
https://github.com/aaronwatters/array_gizmos
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A collection of array operations and visualizations
- Host: GitHub
- URL: https://github.com/aaronwatters/array_gizmos
- Owner: AaronWatters
- License: bsd-2-clause
- Created: 2022-09-09T17:32:24.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2023-11-15T14:38:37.000Z (about 1 year ago)
- Last Synced: 2024-10-14T06:24:46.902Z (2 months ago)
- Language: Python
- Size: 11.8 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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:
```bash
% git clone https://github.com/AaronWatters/jp_doodle.git
% cd jp_doodle
% pip install -e .
% cd ..
```
Install the H5Gizmos dependancy manually in development mode:
```bash
% git clone https://github.com/AaronWatters/H5Gizmos.git
% cd H5Gizmos
% pip install -e .
% cd ..
```
Then install this module in development mode:
```bash
% 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:
```bash
% cd array_gizmos/notebooks/
% compare_npz_labels labels_and_image.npz
Open gizmo using link (control-click / open link)
Click to open
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
### Notes on the "overlayed segmentation" proof of concept (historical/deprecated)