[ome-devel] Super-Resolution standard format

[Seamus Holden]

Nice! HD5 makes a lot of sense, great idea! Much more compact than XML.

Next week, I promise I will submit the various multi-format test data from
lots of different software that we used in PALMsiever development (if I
post this then it will force me to do so!).

Best wishes
Seamus

On Fri, 24 Jul 2015 at 18:24 Simon Li <spli at dundee.ac.uk> wrote:

>   Hi all
>
>  Based on the "Common Headers" section of the spreadsheet that Pedro's
> shared I've written an example python script for storing some of this data
> in OMERO as a HDF5 table:
>
> https://github.com/manics/omero-superresolution-tables
>
>  This isn't in any way complete, and there's plenty of scope for extending
> it, and improving it's useability, but I just throught I'd make a start
> since Ian Munro provided us with some real data.
>
> There are some usage instructions in the README file. The sample file is
> an extract of a larger file from Imperial*- *I'm currently trying the
> script on the full file file with 4 million rows (note some optimisation
> might be needed on the OMERO side, it's taking a while...). Next step is to
> consider adding the points as ROIs in OMERO.
>
>  Enjoy your weekend!
>
>  Simon
>
>
>
> On 25 June 2015 at 09:48, Pedro Almada <pedro.almada.13 at ucl.ac.uk> wrote:
>
>>  Dear all,
>>
>>  Some of the members of the UK Super-Resolution community have discussed
>> the integration of single-molecule localization microscopy data
>> (PALM/STORM) into OMERO and what became completely clear is the need to
>> have a general way to import the output of the localization algorithms.
>> We've made a push towards having a general importer and file-standard by
>> looking at the most common commercial and free software available. The
>> early results are available as a public google doc
>> <https://docs.google.com/spreadsheets/d/1YxC_WBFEvgy5jo__0_DaC6B0kzy9ptOhc2Z284PnRhU/edit?usp=sharing>
>> .
>>
>>  Our goals are to follow the BioFormats route and:
>>  - Create an importer capable of reading most localization data
>>  - Establish a standard, flexible format that the importer would write
>> into.
>>
>>  It's our hope future algorithms would then start using a standard
>> format, since this would finally decouple localization data from the
>> software used to create it. A few advantages to the SR field would come
>> from this:
>>  - Analysis software (eg. clustering) would no longer need to be custom
>> designed for a specific format
>>  - Rendering could finally be decoupled from the localization software,
>> as the output of any algorithm should be compatible with any rendering
>> method.
>>  - Comparison of the output of different algorithms could be efficiently
>> compared analytically and visual biases from different rendering methods
>> would be removed.
>>
>>  We need to publicly discuss how to implement this, and we believe the
>> OMERO developers community is the correct starting point. For now, it seems
>> the minimum headers common to all datasets are X position, Y position and
>> the frame number of the localized particle. Other features are immediately
>> useful such as signal intensity/photon-count but not all formats include it.
>>
>>  There are also questions of implementation. The BIG.EPFL people have
>> tackled this problem
>> <http://bigwww.epfl.ch/smlm/methods/index.html?p=metrics>in a fashion,
>> by creating an XML generator. It asks the user to name the headers, column
>> separation, etc and an XML is created which is used by their comparison
>> software to read any text based file such as .csv or .xls. However, some
>> software packages actually generate binary files and not text based files,
>> which means an extra exporting step is necessary. Also, XML has an
>> associated overhead. I would like to see an importer that can handle the
>> binary data, but have no clue as to how hard that would be to implement (I
>> can share example outputs though).
>>
>>  What do you think?
>>
>>  All the best,
>> Pedro
>>
>> PhD Student
>> Quantitative Imaging and Nanobiophysics Group
>> MRC Laboratory for Molecular Cell Biology
>> University College London
>> Gower Street
>> London
>>  WC1E 6BT
>> Telephone: +44 (0)20 7679 7806
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
>
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>>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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