napari-argos-archive-reader 0.0.4

A plugin to read Dioptic ARGOS archive files

napari-argos-archive-reader

A plugin to read Dioptic ARGOS archive files

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This repo contains a reader plugin for DIOPTIC ARGOS Archive files, which have .zip file extension. Individual ARGOS layers are grouped into napari layer with stacks according to their illumination, stage XY position and Z-stack information.

The plugin implements delayed reading using dask.delayed so that one can quickly see the contents even for large archives with many layers. Note!: switching to volume rendering or swapping axes can trigger the loading of all ARGOS layers, which can take a long time for large archives.

ARGOS is an automated system for surface inspection according to ISO 10110-7.

This plugin is still experimental and does not support all features of ARGOS archives.

Currently, the plugin

• can read Argos matrix archives containing regular image layers including:
  • ✅ segmentation masks
  • ✅ Z-stack metadata
  • ✅ Illumination metadata
  • ✅ proper scaling and affine transformation of layers
• can read ❔✅ Argos line scan (polar) archives with minimal support (no metadata parsing) This has not been tested on many archives.

Not supported are:

• ❌ annotated archives
• ❌ pyramid image structures
• ❌ Line segmentation metadata
• ❌ color metadata
• ❌ ...

Installation

If you have napari installed you can install the plugin from the napari hub through the Plugins -> Plugin Manger menu entry. After waiting a short while for napari to retrieve the plugins available from the hub, simply enter "argos" in the filter line entry field at the top to narrow down the plugin list and click install.

You can install napari-argos-archive-reader via pip:

pip install napari-argos-archive-reader

To install latest development version :

pip install git+https://github.com/dioptic/napari-argos-archive-reader.git

License

Distributed under the terms of the MIT license, "napari-argos-archive-reader" is free and open source software