/bigdataviewer-bioformats

Opens bio-formats images in BigDataViewer

Primary LanguageJavaBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

THE FUNCTIONALITIES OF THIS REPOSITORY ARE MOVED TO https://github.com/BIOP/bigdataviewer-image-loaders

BigDataViewer Bio-Formats Bridge

This repository enables the opening of files into BigDataViewer by using the Bio-Formats API. Emphasis has been put on correct support of metadata for locating multiple series of acquisition, like in slide scanner file.

Multiresolition file formats supported by BioFormats are translated into a BigDataViewer multiresolution source, enabling support for 'big' files.

Note: signed pixels values are not supported.

Usage in ImageJ/Fiji

BigDataViewer-BioFormats is shipped with the Bigdataviewer-Playground update site.

Fiji Plugins List

Open [BioFormats Bdv Bridge]

Support bioformats multiresolution api. Attempts to set colors based on bioformats metadata. Do not attempt auto contrast.

Input

  • [String] datasetname:Name of this dataset
  • [File[]] files:Dataset files

Output

  • [AbstractSpimData] spimdata

Open [BioFormats Bdv Bridge (Basic)]

Support bioformats multiresolution API. Attempts to set colors based on bioformats metadata. Do not attempt auto contrast.

Input

  • [String] datasetname:Name of this dataset
  • [File[]] files:Dataset files
  • [boolean] splitrgbchannels:Split RGB channels
  • [String] unit:Physical units of the dataset

Output

  • [AbstractSpimData] spimdata

Export Sources To OME Tiff (build pyramid)

Saves Bdv sources as a multi-channel OME-Tiff file, with multi-resolution levels recomputed from the highest resolution level

Input

  • [int] downscaling:Scaling factor between resolution levels
  • [File] file:Output file
  • [Boolean] lzw_compression:Use LZW compression
  • [int] max_tiles_queue:Number of tiles computed in advance
  • [int] n_resolution_levels:Number of resolution levels
  • [int] n_threads:Number of threads (0 = serial)
  • [SourceAndConverter[]] sacs:Sources to export
  • [int] tile_size_x:Tile Size X (negative: no tiling)
  • [int] tile_size_y:Tile Size Y (negative: no tiling)
  • [String] unit:Physical unit

Export Sources To OME Tiff

Saves Bdv sources as a multi-channel OME-Tiff file, keeping original multiresolution levels if the sources are initially multiresolution.

Input

  • [File] file:Output file
  • [Boolean] lzw_compression:Use LZW compression
  • [int] max_tiles_queue:Number of tiles computed in advance
  • [int] n_threads:Number of threads (0 = serial)
  • [SourceAndConverter[]] sacs:Sources to export
  • [int] tile_size_x:Tile Size X (negative: no tiling)
  • [int] tile_size_y:Tile Size Y (negative: no tiling)
  • [String] unit:Physical unit

Open sample dataset

Open sample datasets Downloads and cache datasets on first open attempt.

Input

  • [String] datasetName:Choose a sample dataset

Output

  • [AbstractSpimData] spimData

Open File with Bio-Formats

Support bioformats multiresolution api. Attempts to set colors based on bioformats metadata. Do not attempt auto contrast.

Input

  • [File] file:File to open
  • [boolean] splitrgbchannels:Split RGB channels if you have 16 bits RGB images
  • [String] unit:Physical units of the dataset