Adding Microscopy support to your existing "openBIS for HCS" server
To activate browsing Microscopy data, you have to:
- Application Server
add a line in
MICROSCOPY_IMAGEdata set type using the Web Browser
add following lines to
or as a core plugin of type
Python Dropbox Configuration
Configuration is similar to screening.
Datastore Server Configuration
Create a core plugin of type
incoming-root-diris defined in
- the Jython drop box script file
If the folder
incoming-microscopy doesn't exist it will be created on DSS start up.
Jython Script Configuration
The main difference between microscopy drop box and screening drop box is that images are not connected to wells anymore.
This has to be specified by invoking in the script
There is a convenience class
SimpleImageContainerDataConfig which maps image identifier attributes to image meta data properties.
Here is an example:
Registration of many data sets for one image container file
An image container file might contain images which should be assigned to different data sets. Instead of making a copy of the image container file (which can be 100 MB or more) there is a way to have this file only once in the data store. Here is a snipped of Jython code which does the trick:
This code assumes
num_series image series in the image container file
fileName. There is a class
SimpleImageContainerDataConfig declared somewhere above the code snippet which knows how to get configuration data from the image container file.
From the first series a normal image data set is created with
createNewImageDataSet. Also the image container file is moved to this image data set. Effectively an image data set container is created which has a physical data set for the image container file. Depending on the configuration also thumbnail data sets are created and part of the image data set container.
For all other series of the image container file the method
createNewImageDataSetFromDataSet is used to create the corresponding image data set. Instead of a file it gets the image data set created first as an argument. It takes physical data set with the big image container file and adds it to the newly created data set. Thus, the physical data set with the image container file will be a component in
num_series image data set containers.
Deprecated - preconfigured dropboxes
to import images with tiles/timepoints/depth scans/channels one has to configure a new drop box using a new
MicroscopyStorageProcessorstorage processor, e.g.:
data-set-info-extractorconfiguration is the same as for any other drop box.
MicroscopyImageFileExtractorsupports following images naming convention:
So valid file names are e.g.: s1_z3_t5_cDAPI.png, s4_cGFP.gif, s3_z19.23_cGFP.gif
To support different naming conventions a new plugin has to be written.
to import images with any naming convention use the following drop box configuration: