(This group is the result of merging the two IWG subgroups GSML and IOEDF. 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:

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, https://doi.org/10.1038/s41596-020-00478-x; MINA, https://doi.org/10.1038/s41596-021-00518-0; Hi-M, https://doi.org/10.1016/j.molcel.2019.01.011; seqFISH+, https://doi.org/10.1038/s41586-019-1049-y; OligoFISSEQ, https://doi.org/10.1038/s41592-020-0890-0; DNA-MERFISH, https://doi.org/10.1016/j.cell.2020.07.032; and IGS).

2) Single-Molecule Localization Microscopy (SMLM) for volumetric imaging, such as OligoSTORM and OligoDNA-PAINT.In this context, we will establish 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 (specifically 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 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 for comments in two versions:

1. General description

2. Specifications

Point people/organizers: Alistair Boettiger, Steve Wang

4DN Google Drive folder: https://drive.google.com/drive/folders/1Rzn7_U_Id81LIHdu0ECcQ5Wc7sBLTqvW?usp=sharing

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

Agenda/Minutes: https://docs.google.com/document/d/1AadO9SjxAEjflAfYq5tdQ1u0OkJtAa_xBhQOk97f8Rk/edit?usp=sharing

Meeting attendee spreadsheet: https://docs.google.com/spreadsheets/d/1Q5PRijFtDwXanWL3caU8LHF1iouKhNR0w7HjWw-9PKg/edit?usp=sharing

Email list: image@4dnucleome.org

Slack channel: swg-imaging-omics-exchange-data-formats

This sub-group of the Imaging Working Group will develop recommended data formats and metadata specifications for sharing 3D chromatin folding traces obtained from multiplexed DNA FISH and other in-situ imaging-based omics approaches, with the flexibility to include additional multi-omic imaging data to be mapped to these structural data, such as RNA expression, protein distribution, cell morphology, or tissue coordinates.

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:

1. General description

2. Specifications