[ome-devel] Super-Resolution standard format

[Simon Li]

Dear Alex

Thanks for adding your file formats. As you might've seen earlier in this thread I made a start on a Python script for importing some SR data into OMERO.tables, which is essentaily HDF5 behind the scenes with some OMERO-specific conventions (in terms of metadata inside the HDF5). Our current (tentative) plans are to stick with this, but remove the OMERO-specific requirements.

https://github.com/manics/omero-superresolution-tables

Ian Munro has done some work on getting PALM-siever and ThunderSTORM to work with this format.

Where we could really use your help is in getting everyone to agree on what columns should be mandatory, their types (for example, should x/y/z always be in nm), and anything else we might've missed.

Best wishes

Simon


On 15 September 2015 at 16:06, Alex Herbert <a.herbert at sussex.ac.uk<mailto:a.herbert at sussex.ac.uk>> wrote:
Dear All,

I am the developer of the super-resolution software we use at the GDSC,
University of Sussex. I'm interested in developing a more universal
format for localisation results. My software currently has its own
format and will load localisations using a few other formats too.
Establishing a common format would greatly improve the analysis of data.

I have added details of my current file formats to the table created by
Pedro Almada:
https://docs.google.com/spreadsheets/d/1YxC_WBFEvgy5jo__0_DaC6B0kzy9ptOhc2Z284PnRhU/edit?usp=sharing

In short there is a self-documenting text format (using a header) of
tab-delimited column data, one line per localisation; and a binary
format that attempts to be self-documenting (using a header) but is
probably not easy to read outside of Java, although the source code is
available to help understand it.

The files store many fields that are specific to the fitting algorithm
used. However the position, estimated signal in photons, and original
image dimensions (including pixel sizes) can be extracted from the file.
These are the principle data that should be useful to other software.
Without the original image dimensions the results are reduced to a set
of localisations floating in a space defined by their bounding box. This
is not ideal for reconstructing an image or performing density analysis.

Regards,

Alex

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