(This group emerged from the merging of the two previously existing GSML and IOEDF IWG subgroups. The wiki pages of the two subgroups were merged on 11.18.21)

Point people/organizers: Sarah Aufmkolk, Alistair Boettiger, Josh Moore, Nicola Neretti, Caterina Strambio-De-Castilla, Steve Wang

4DN Google Drive folder: https://drive.google.com/drive/folders/1dmAasW0riD3nyfODbQJefdFw1yRK4dpd?usp=sharing

4DN Calendar: https://wiki.4dnucleome.org/4dn:calendar_4dn

Agenda/Minutes: https://docs.google.com/document/d/1N8iRYV7cpF60rHMoPW1aaHi11v1_YxluB_0iWNCS0ck/edit?usp=sharing

Meeting attendee spreadsheet: https://docs.google.com/spreadsheets/d/1i3yd_mAioaiFFLOpUkqV0HY0OM0nP1-1jmox4FF-0UY/edit?usp=sharing

Email list: image@4dnucleome.org

Slack channel: #swg-fish-omics-exchange-data-formats

Renaming the Merged IOEDF + GSMLDF Subgroup (Mission Statement PDF)

A key output of the 4DN project is the open exchange of datasets related to the structure of the human cell nucleus and the genome within. Recent years have seen a rapid expansion of FISH-omics methods, which quantify the spatial organization of DNA, RNA, and protein in the cell and provide an expanded understanding of how higher-order chromosome structure relates to transcriptional activity and cell development. Despite this progress, FISH-based image data are not yet routinely made public upon scientific publication because of the lack of common specifications for data exchange. This challenge is experienced across the bioimaging community as a result, a solution built, tested, and proven in 4DN can have a wide impact all over the world.
Central to addressing this hurdle is the work carried out by the 4DN Imaging Working Group (IWG) in collaboration with the 4DN-DCIC , the Imaging and Omics Working Group (IOWG), and the Open Microscopy Environment initiative to support the accessibility and exchange of FISH Omics data. This will include the development of community specifications for image-data formats, quality control and documentation (i.e., provenance) metadata, and shared data management and analysis pipelines.

The mission of this sub-group of the IWG will focus on establishing standardized data formats for typical multiplexed FISH Omics data, and metadata specifications to promote optimized analysis and data exchange.

Specific attention will be devoted to making sure specifications will be flexible enough to include other in-situ imaging-based omics approaches, and will be extensible enough to permit the description of additional multi-omic imaging data to be mapped to these structural data, such as RNA expression, protein distribution, cell morphology, or tissue coordinates.

We will specifically focus on two initial types of experiments:

1) Three-dimensional (3D) Chromatin Tracing (CT) experiments in which polymer tracing algorithms are used to string together the localization of individual DNA bright Spots to reconstruct the three-dimensional (3D) path of chromatin fibers (e.g., ORCA; MINA; Hi-M; seqFISH+; OligoFISSEQ; DNA-MERFISH; and IGS).

2)Single-Molecule Localization Microscopy (SMLM) for volumetric imaging [1], such as OligoSTORM and OligoDNA-PAINT. In this context, in order to support the exchange of results from genomic super-resolution imaging efforts, we will focus on the following individual tasks:

1. Establishment of data models that capture the output of typical OligoSTORM single-molecule localization microscopy (SMLM) data.
2. Establishment of clear metadata specifications to promote scientific rigor, reproducibility, data exchange, and analysis.
3. Establishment of pipelines exemplifying the conversion of Single-Molecule Location Microscopy (SMLM) image and localization data from the proprietary Bruker binary data format to a cloud-optimized OME-NGFF format (more specifically OME-Zarr ) [2] and showcase the analysis from the Zarr-file format with software tools likeintegrative modeling of genomic regions (IMGR) [1].

It should be noted that this effort will support super-resolved and widefield data being acquired with Bruker Vutara 352 or Vutara VXL microscopes, but welcomes data produced from other imaging platforms!

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 fon our ReadTheDoc page and on GitHub:

• Please refer to theReadTheDocs pagefor any and all information about this format and to download example files to get started.
• Please report any questions, issues, and proposals for change on theGitHub issue page

IMPORTANT: All previous GoogleDoc and GoogleSheet representations of FOF-CT are now deprecated and no longer maintained.

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The working group is currently engaged in the definition of exchange formats that allow the exchange of data emerging from OligoPaint and OligoSTORM experiments. This includes defining a data model for FOF experiments and drafting the FOF-GFML specifications. The current status of work can be found below:

1. FOF Data Model