Bioformats Image MyTardis Filter

Only dm3, ims, jp2, lif, nd2, tif and vsi files are supported for now. However, Bioformats supports many formats so potentially so will this filter without much effort.

Filter for generating image thumbnails and storing metadata for MyTardis using LOCI Bioformats' command line binaries that interact with their jar file.

Todo

• Support more file types
• Error handling if the Bioformats tool (bfconvert or showing) fails for whatever reason
• More detailed metadata parameters than simple text output

Requirements

• Java Runtime Environment
• MyTardis 3.6 Branch
• http://cvs.openmicroscopy.org.uk/snapshots/bioformats/4.4.6/bftools.zip
• http://hudson.openmicroscopy.org.uk/job/BIOFORMATS-trunk/lastSuccessfulBuild/artifact/artifacts/loci_tools.jar

Installation

• Unzip bftools.zip into a directory on the MyTardis server
• Place loci_tools in the same directory as the unzipped bftools
• Make sure the MyTardis web server user can read the bftools' directory contents

Git clone this repository into /path/to/mytardis/tardis/tardis_portal/filters:

git clone git@github.com:wettenhj/bioformatsimage-mytardis-filter.git bioformatsimage

Add the following to your MyTardis settings file eg. /path/to/mytardis/tardis/settings.py

MIDDLEWARE_CLASSES = MIDDLEWARE_CLASSES + ('tardis.tardis_portal.filters.FilterInitMiddleware',)

FILTER_MIDDLEWARE = (("tardis.tardis_portal.filters", "FilterInitMiddleware"),)

The above enables the filter middleware for all actions.

Then add the definition for this filter.

POST_SAVE_FILTERS = [
   ("tardis.tardis_portal.filters.bioformatsimage.bioformatsimage.make_filter",
   ["BIOFORMATS", "http://tardis.edu.au/schemas/bioformats/1",
    "/path/to/bftools/bfconvert",
     "/path/to/bftools/showinf"]),
   ]

If you want to specify the name of the Celery queue the Bioformats processes should run in (e.g. "filters"), you can do so as follows:

POST_SAVE_FILTERS = [
   ("tardis.tardis_portal.filters.bioformatsimage.bioformatsimage.make_filter",
   ["BIOFORMATS", "http://tardis.edu.au/schemas/bioformats/1",
    "/path/to/bftools/bfconvert",
     "/path/to/bftools/showinf"]),
   {'queue': 'filters'}
   ],

Where the bftools directory is correct for your installation.

cd /path/to/mytardis and load the parameter schema into the MyTardis database:

bin/django loaddata tardis/tardis_portal/filters/bioformatsimage/bioformats.json

Restart MyTardis. From now on, all dm3, ims, jp2, lif, nd2, tif and vsi files loaded will have preview images and metadata extracted and stored alongside the file itself.