# napari-argos-archive-reader
[](https://github.com/dioptic/napari-argos-archive-reader/raw/main/LICENSE)
[](https://pypi.org/project/napari-argos-archive-reader)
[](https://python.org)
[](https://github.com/dioptic/napari-argos-archive-reader/actions)
[](https://codecov.io/gh/dioptic/napari-argos-archive-reader)
[](https://napari-hub.org/plugins/napari-argos-archive-reader)
A plugin to read Dioptic ARGOS archive files
----------------------------------
This repo contains a reader plugin for [DIOPTIC ARGOS](https://www.dioptic.de/en/argos-en/) 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](https://www.dioptic.de/en/argos-en/) 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
* ❌ ...
## Usage
### Opening files
Simply drag and drop an ARGOS Archive `.zip` file onto the napari canvas or use `File->Open` to open it.
### Synchronizing contrast limits
By default, after reading an archive, each napari layer will have their own contrast limits, so you can
adjust these contrast limits individually.
The reader plugin registers a custom key binding after reading an ARGOS archive. Pressing the `s` key will allow
you to synchronize the contrast limits for a set of layers:
* If you select _a single_ napari layer corresponding to an image/stack from an ARGOS archive, all napari image
layers that were loaded from this archive now have their contrast limits synchronized, i.e. changing the
contrast limits of _any_ of them will adjust the contrast limits of _all_ of the layers belonging to the same
archive.
* If you select _multiple_ napari layers and press `s` all of these and only these napari layers will have
their contrast limits synchronized, regardless of whether they belong to the same ARGOS archive or not.
## 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
[MIT]: http://opensource.org/licenses/MIT
[pip]: https://pypi.org/project/pip/
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"description": "# napari-argos-archive-reader\n\n[](https://github.com/dioptic/napari-argos-archive-reader/raw/main/LICENSE)\n[](https://pypi.org/project/napari-argos-archive-reader)\n[](https://python.org)\n[](https://github.com/dioptic/napari-argos-archive-reader/actions)\n[](https://codecov.io/gh/dioptic/napari-argos-archive-reader)\n[](https://napari-hub.org/plugins/napari-argos-archive-reader)\n\nA plugin to read Dioptic ARGOS archive files\n\n----------------------------------\n\nThis repo contains a reader plugin for [DIOPTIC ARGOS](https://www.dioptic.de/en/argos-en/) Archive files, which\nhave `.zip` file extension.\nIndividual ARGOS layers are grouped into napari layer with stacks according to\ntheir illumination, stage XY position and Z-stack information.\n\nThe plugin implements delayed reading using `dask.delayed` so that one can quickly\nsee the contents even for large archives with many layers. Note!: switching to\nvolume rendering or swapping axes can trigger the loading of all ARGOS layers, which\ncan take a long time for large archives.\n\n[ARGOS](https://www.dioptic.de/en/argos-en/) is an automated system\nfor surface inspection according to ISO 10110-7.\n\nThis plugin is still experimental and does not support all features of ARGOS archives.\n\nCurrently, the plugin\n\n* can read Argos matrix archives containing regular image layers including:\n * \u2705 segmentation masks\n * \u2705 Z-stack metadata\n * \u2705 Illumination metadata\n * \u2705 proper scaling and affine transformation of layers\n* can read \u2754\u2705 Argos line scan (polar) archives with minimal support (no metadata parsing)\nThis has not been tested on many archives.\n\nNot supported are:\n\n* \u274c annotated archives\n* \u274c pyramid image structures\n* \u274c Line segmentation metadata\n* \u274c color metadata\n* \u274c ...\n\n## Usage\n\n### Opening files\n\nSimply drag and drop an ARGOS Archive `.zip` file onto the napari canvas or use `File->Open` to open it.\n\n### Synchronizing contrast limits\n\nBy default, after reading an archive, each napari layer will have their own contrast limits, so you can\nadjust these contrast limits individually.\n\nThe reader plugin registers a custom key binding after reading an ARGOS archive. Pressing the `s` key will allow\nyou to synchronize the contrast limits for a set of layers:\n\n* If you select _a single_ napari layer corresponding to an image/stack from an ARGOS archive, all napari image\nlayers that were loaded from this archive now have their contrast limits synchronized, i.e. changing the\ncontrast limits of _any_ of them will adjust the contrast limits of _all_ of the layers belonging to the same\narchive.\n* If you select _multiple_ napari layers and press `s` all of these and only these napari layers will have\ntheir contrast limits synchronized, regardless of whether they belong to the same ARGOS archive or not.\n\n## Installation\n\nIf you have napari installed you can install the plugin from the napari hub through the `Plugins -> Plugin Manger` menu\nentry. After waiting a short while for napari to retrieve the plugins available from the hub, simply enter \"argos\" in\nthe filter line entry field at the top to narrow down the plugin list and click install.\n\nYou can install `napari-argos-archive-reader` via [pip]:\n\n pip install napari-argos-archive-reader\n\nTo install latest development version :\n\n pip install git+https://github.com/dioptic/napari-argos-archive-reader.git\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"napari-argos-archive-reader\" is free and open source software\n\n[MIT]: http://opensource.org/licenses/MIT\n[pip]: https://pypi.org/project/pip/\n",
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