2017-12-04 - Fiji + KNIP hackathon
From Monday, December 4, 2017 through Friday, December 15, 2017, the Max Planck Institute of Molecular Cell Biology and Genetics hosts ~50 developers at the Center for Systems Biology in Dresden, Germany for a hackathon to develop ImageJ2 and Fiji core infrastructure and plugins.
Voluntary hackathon calendar
Hackathon google doc
Hackathon on Twitter (#hackdd17)
H5, not HDF5
For more info on H5, check out the github repository here.
- feels like HDF5, but stores chunks(blocks) in separate files in the file system.
- is a Java library, but Constantin Pape already wrote a C++/python version of it: z5 (also matches "zarr" library), https://github.com/constantinpape/z5
- attributes are stored in an additional JSON file
- Discussion: should we define standard now as to how data should be stored in there to prevent an emergence of a zoo of different flavors as there is for HDF5?
- how to do time series where each timestep / angle could have different image size
- if we want a general "N5 viewer" for images, we'd have to add calibration data
- put this information around the N5 dataset, because it behaves more like a dataset within an H5 file.
- Perhaps make it versioned? Because a duck is not always a duck...
- why another file format?
- parallel writes (awesome for clusters with shared filesystem)
- there is a special type for label blocks
- blocks can have a halo
- the block grid does not need to be filled dense, some blocks could be missing
- couldn't this just be another flavor of HDF5?
- are parallel writes to the same block prevented by some kind of locks?
- the HDF5 team should be included in the discussions to learn from their mistakes - there is lots of information on parallel writing of HDF5 files out there