knowledgevis / large_image

Python modules to work with large multiresolution images.

Large Image

Python modules to work with large multiresolution images.

Quick Installation via pip

In addition to installing the large-image package, you'll need at least one tile source (a large-image-source-xxx package). You can install everything from the main project with one of these commands:

• Install all tile sources and all Girder plugins on linux: pip install large-image[all] girder-large-image-annotation[tasks] --find-links https://girder.github.io/large_image_wheels
• Install all tile sources on linux: pip install large-image[all] --find-links https://girder.github.io/large_image_wheels

Modules

Large Image consists of several Python modules designed to work together. These include:

• large-image: The core module. You can specify extras_require of the name of any tile source included with this repository, sources for all of the tile sources in the repository, memcached for using memcached for tile caching, or all for all of the tile sources and memcached.

• girder-large-image: Large Image as a Girder 3.x plugin. You can specify extras_require of tasks to install a Girder Worker task that can convert otherwise unreadable images to pyramidal tiff files.

• girder-large-image-annotation: Annotations for large images as a Girder 3.x plugin.

• large-image-tasks: A utility for using pyvips to convert images into pyramidal tiff files that can be read efficiently by large_image. This can be used by itself or with Girder Worker.

• Tile sources:

  • large-image-source-tiff: A tile source for reading pyramidal tiff files in common compression formats.
  • large-image-source-openslide: A tile source using the OpenSlide library. This works with svs, ndpi, Mirax, tiff, vms, and other file formats.
  • large-image-source-ometiff: A tile source using the tiff library that can handle some multi-frame OMETiff files.
  • large-image-source-pil: A tile source for small images via the Python Imaging Library (Pillow).
  • large-image-source-gdal: A tile source for reading geotiff files via GDAL. This handles source data with more complex transforms than the mapnik tile source.
  • large-image-source-mapnik: A tile source for reading geotiff and netcdf files via Mapnik and GDAL. This handles more vector issues than the gdal tile source.
  • large-image-source-openjpeg: A tile source using the Glymur library to read jp2 (JPEG 2000) files.
  • large-image-source-nd2: A tile source for reading nd2 (NIS Element) images.
  • large-image-source-bioformats: A tile source for reading any file handled by the Java Bioformats library.
  • large-image-source-test: A tile source that generates test tiles, including a simple fractal pattern. Useful for testing extreme zoom levels.
  • large-image-source-dummy: A tile source that does nothing.

  Most tile sources can be used with girder-large-image.

Installation

To install all packages from source:

1. Clone the repository:

   git clone https://github.com/girder/large_image.git

   Change to the source directory:

   cd large_image

2. Install all packages and dependencies:

   pip install -e .[memcached] -r requirements-dev.txt

Tile source prerequisites

Many tile sources have complex prerequisites. These can be installed directly using your system's package manager or from some prebuilt Python wheels for Linux. The prebuilt wheels are not official packages, but they can be used by instructing pip to use them by preference:

pip install -e .[memcached] -r requirements-dev.txt --find-links https://girder.github.io/large_image_wheels

Migration from Girder 2 to Girder 3

If you are migrating a Girder 2 instance with Large Image to Girder 3, you need to do a one time database update. Specifically, one of the tile sources' internal name changed.

Access the Girder Mongo database. The command for this in a simple installation is:

mongo girder

Update the tile source name by issuing the Mongo command:

db.item.updateMany({"largeImage.sourceName": "svs"}, {$set: {"largeImage.sourceName": "openslide"}})