bftools

Singularity recipe for bftools.

showinf. Prints information about a given image file to the console, and displays the image itself in the Bio-Formats image viewer (see Displaying images and metadata for more information).
ijview. Displays the given image file in ImageJ using the Bio-Formats Importer plugin. See Display file in ImageJ for details.
bfconvert. Converts an image file from one format to another. Bio-Formats must support writing to the output file (see Converting a file to different format for more information).
formatlist. Displays a list of supported file formats in HTML, plaintext or XML. See List supported file formats for details.
xmlindent. A simple XML prettifier similar to xmllint --format but more robust in that it attempts to produce output regardless of syntax errors in the XML. See Format XML data for details.
xmlvalid. A command-line XML validation tool, useful for checking an OME-XML document for compliance with the OME-XML schema. See Validating XML in an OME-TIFF for details.
tiffcomment. Dumps the comment from the given TIFF file’s first IFD entry; useful for examining the OME-XML block in an OME-TIFF file (also see Editing XML in an OME-TIFF).
domainlist. Displays a list of imaging domains and the supported formats associated with each domain. See List formats by domain for more information.
mkfake. Creates a “fake” high-content screen with configurable dimensions. This is useful for testing how HCS metadata is handled, without requiring real image data from an acquired screen. See Create a high-content screen for testing for more information.

To make this image even more awesome I included ffmpeg and ImageMagick.

Pre-requisites

Singularity v3.5.+.

Building the image using the recipe

To build the image locally

Run the script build.sh to build image locally.

bash ./build.sh

To build the image remotely remotely

Run the script rbuild.sh to build image remotely.

bash ./rbuild.sh

You will need to edit the script above to match your account on SyLabs.io.

Pulling from the repository

If you have the client installed and cannot build the image locally nor remotely, simply run

singularity pull --arch amd64 library://icaoberg/default/bioformats:v6.3.1

Disclaimer

I am nothing but a humble programmer creating the container for these wonderful apps. To meet the amazing team behind Bio-Formats click here.

icaoberg / singularity-bftools