About

From Endrov

Endrov started development in 2007 by Johan Henriksson in the group of Thomas B├╝rglin group / Karolinska insitutet. At that time it was merely a tool to support the analysis of C. elegans embryogenesis. It was decided to not base it on ImageJ because little of it could be reused, many of the problems came from the core design. Since then the scope of Endrov has expanded to be useful for all image processing and be able to replace ImageJ.

Some of the things we want to address are:

  • Unity, all pieces should fit together into a solid framework. No plugin should appear as a program within a program. This also means plugins will interact more and there should be no code duplication.
  • A common way of handling metadata, such as custom annotation of images. This should not introduce new file formats but rather use the framework to be future compatible with new file formats and image servers. Metadata is also given the same treatment as images, and are well-defined objects.
  • Ability to handle large recordings, in the 100GB range and above. This means an operation cannot be applied to everything just to see the result because it would take too much time; Endrov hides the size by using lazy evaluation.
  • Ability to handle high-dimensional data. This means 5D + multiple positions + wells + more.
  • The Photoshop-like way of working does not make sense for interactive image processing - one always wants to keep track of all intermediate results and the original data. This meant the entire user workflow has changed and all operations are done through Flows.
  • One community, one software. The ImageJ plugins were spread around over the web, many without source and with problematic licenses. We will keep everything in one location. This will make it much more feasible to evolve the core design and hence we can tackle also the requirements of tomorrow.
  • Integrated microscopy; besides finally having a standard program for microscopy, this leverages online image analysis which will become more interesting in the future.

Initially we have had our own file format (OST) but we are now moving toward OME-TIFF together with extensions to allow our custom metadata to be written out. We encourage everyone to use OMERO to keep track of all their images.

Site

This main contact for the software and website is Johan Henriksson, (mahogny@@@REMOVE@@@areta.org). See otherwise our mailing list and chat channels for contact.