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Genomic Single-Molecule Localization Data Formats
This sub-group has now been merged with the ImagingOmics Exchange Data Formats sub-group of the Imaging Working Group.
Point people/organizers: Sarah Aufmkolk, Alistair Boettiger, Joshua Moore, Nicola Neretti, Caterina Strambio De Castilla
4DN Google Drive folder: https://drive.google.com/drive/folders/1a7nPmVc2pfIy3TuHz-SVgZ4YdFrxr3je?usp=sharing
4DN Calendar: https://wiki.4dnucleome.org/4dn:calendar_4dn
Agenda/Minutes: https://docs.google.com/document/d/1TN3ImqvPTxQ1qSreYkcgCU_chO4CoJK2no7vYmxyg0I/edit?usp=sharing
Meeting attendee spreadsheet: https://docs.google.com/spreadsheets/d/1ZMDy-LT6rcRS_kmSqfA07Fja469NNpyjWHqCQnTX_90/edit?usp=sharing
Email list: image@4dnucleome.org
Slack channel:
Mission Statement
“Genomic single-molecule localization data formats (GSML data formats): data sharing and format conceptualization for server-based storage”
This working group aims to support the accessibility of genomic super-resolution imaging efforts. We will focus on establishing the structure of typical OligoSTORM [1] single-molecule localization microscopy (SMLM) data, establishing clear meta-data descriptions that allow optimized analysis and data-sharing. Furthermore, we will establish pipelines exemplifying the conversion of SMLM image and localization data from the proprietary Bruker binary data format to a cloud-optimized OME-Zarr format [2] and showcase the analysis from the zarr-file format with software tools like IMGR [1].
It should be noted that this effort will support super-resolved and widefield data being acquired with Bruker Vutara or VXL microscopes, but welcomes to include other SMLM data formats!
This effort will be organized in close alliance with the Open Microscopy Environment consortium and the 4DN data repository.
Output
FISH Omics Format for Chromating Tracing (FOF-CT)
The first output of this sub-group is the proposed FISH Omics Format for Chromating Tracing (FOF-CT). We encourage the community to provide feedback ahead to approval from the November Steering Committee meeting. The format is available for comments in two versions: