https://github.com/alleninstitute/asap-modules

Shared repo for EM connectomics and Array Tomography render based image processing modules
https://github.com/alleninstitute/asap-modules

Last synced: 12 months ago
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Shared repo for EM connectomics and Array Tomography render based image processing modules

• Host: GitHub
• URL: https://github.com/alleninstitute/asap-modules
• Owner: AllenInstitute
• License: bsd-2-clause
• Created: 2017-08-23T16:03:12.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2025-03-25T01:08:36.000Z (over 1 year ago)
• Last Synced: 2025-07-07T12:07:14.810Z (12 months ago)
• Language: Python
• Homepage: https://asap-modules.readthedocs.io/
• Size: 113 MB
• Stars: 15
• Watchers: 12
• Forks: 5
• Open Issues: 15
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

          
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# ASAP-modules

ASAP is a set of modules to perform stitching and alignment of EM and Array tomography data.

It is suitable for processing large-scale datasets and supports multiple computational environments.

# Documentation

The complete documentation is available [here](https://asap-modules.readthedocs.io)

# Installation

Please refer the documentation [Installation](docs/readme/installation.rst). on how to install and use ASAP modules

# How to run

The order of processing is as follows; 

1. [Lens correction](docs/readme/lens_correction.rst)

2. [Mipmap generation](docs/readme/mipmaps.rst)

3. [Montaging](docs/readme/montaging.rst)

4. [Global 3D alignment](docs/readme/rough_alignment.rst)

# Other Modules

A few other modules are included in ASAP to do the following.

1. Materialization - render intermediate/final aligned volume to disk

   for further processing

2. Fusion - Fuse global 3D non-linear aligned chunks together to make a

   complete volume

3. Point match filter - A module that performs point match filtering of

   an existing point match collection

4. Point match optimization - Performs a parameter sweep from a given

   set of ranges on a random sample of tilepairs to identify the optimal

   set of parameters

5. Registration - Register individual sections in an already aligned

   volume (useful in cases of aligning missing/reimaged sections)

# Support

We are planning on occasional updating this tool with no fixed schedule. 

Community involvement is encouraged through both issues and pull requests. 

Please make pull requests against the dev branch, as we will test changes 

there before merging into master.

# Acknowledgments

This project is supported by the Intelligence Advanced Research Projects

Activity (IARPA) via Department of Interior / Interior Business Center

(DoI/IBC) contract number D16PC00004. The U.S. Government is authorized

to reproduce and distribute reprints for Governmental purposes

notwithstanding any copyright annotation theron.

Disclaimer: The views and conclusions contained herein are those of the

authors and should not be interpreted as necessarily representing the

official policies or endorsements, either expressed or implied, of

IARPA, DoI/IBC, or the U.S. Government.

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