Data and Image Analysis Special Interest Group Meeting,
SBS 15th Conference – Lille, France
April 28, 2009
Topic of this meeting was to discuss standards in HCS. There were approximately 30 attendees with a surprising lack of vendors, except for BD and MDS. There was one SBS board member, who has attended out of interest but is not involved at the SBS level in these discussions. It transpired that no board member is in charge of the HCS standard discussion within SBS; Sandra Nelson will bring this to the attention of the SBS board members.
It was reported that ISAC (International Society for Advancement of Cytometry) has become active in creating a standard for the HCS community. A telephone conference was taking place the same day amongst active members. Contact with ISAC has been established and the efforts should be joined in the future.
After an introduction about what was done and discussed about standards in the past, the discussion focused on what should be done in the future. There was again an agreement amongst users that a standard file format for images should be defined to allow accessing image data using different software packages. The idea is to create a standard tif file containing metadata either in the header or the footer of the file. The metadata should be in xml format. What metadata should be put in the file was next discussed. Metadata could contain information on the setting of the microscope, but beyond that, also information about the experimental conditions (compound identity and concentration, time point, etc.) and the assay (cell line, target, stain used, event being monitored, etc.)
There was a general agreement that the metadata should be simple and cover only the most basic settings of the hardware. The reasons for this are two-fold:
1. The image file size should not grow too much, given the amount of data generated; 2. Out of pragmatism, it is better to split the tasks at hand into small manageable chunks to allow the speedy establishment of a file standard. In order to still have access to the other metadata, a link should be built into the xml file pointing to another xml file containing the more general information. What information is deemed minimal for the tif xml file needs to be discussed amongst users. To this end a consortium should be assembled consisting of users and vendors and would propose a set of information that should be found in the xml file of each image file. Several file formats have been proposed in the past and it was thought that OME tif should be adopted by the HCS community and the minimal information xml of Ilya Ravkin should also be considered. To allow the user community to have insight and share their opinion concerning this process, a wiki site has been put up by the MPI-CBG and can be found at:
The site will have posts on the HCS standard and the users could then voice their opinion whether they would like it modified, shortened or expanded. This process should not be indefinite and a deadline should be set to have a first version of the file within a year. It would then be up to the vendors to adopt this file format and write the necessary code for the microscope to store the relevant metadata automatically in the tif file.
Concerning the further metadata, the OME community has come up with a xml file for storing information relevant to a screen called ScreenPlateWell (SPW). This would be a good starting point for creating a standard screening xml file and will be also be posted on the wiki site. A proposal for an assay xml file, an image analysis xml file, a statistical treatment of data xml file and a semantic description of the phenotype xml file would also be welcome. These efforts should come after the establishment of the most basic tif standard, as this is the most needed at this time.
The terms to be used in the xml file should
be taken from existing ontologies and only when no term has been
defined, should a new ontology be created.
Software needs to be created to enter information in the various xml files and programmers need to take on that task.
Given the amount of work to be done, it was
agreed that getting funding would be beneficial and that a team
dedicated to this task would be much more efficient. The
standards initiative within the HCS community has been very
slow, partly due to our ignorance of the process but also due to
the lack of time of the different actors to both fulfill their
regular duties and take on the added burden of standards in HCS.
Several sources of funding are possible, the EU, CHI, SBS could
also contribute some funds and certainly more sources of funding
could be found.
1. Form a committee/consortium for users/vendors to agree on standards, interested people should send email to Marc Bickle: email@example.com
2. Find a SBS board member to follow the standards issue
3. Send the HCS standards wiki site to the community
4. Post on the wiki the OME xml and Ilya Ravkin’s xml
5. Review potential funding/resourcing approaches: 1) clear & concise proposal to SBS to hire a consultant to drive the initiative; 2) possible European Union funding; 3) hire CHI organization to evaluate and drive standardization process
6. Obtain feedback from ISAC conference
Chair: Marc Bickle, MPI-CBG, firstname.lastname@example.org
Co-Chair: David Burns, Abbot Laboratories email@example.com