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--- 4dn:phase2:working_groups:imaging:fish_omics_exchange_data_formats [2021/11/19 18:50]
caterina_str [Output]
+++ 4dn:phase2:working_groups:imaging:fish_omics_exchange_data_formats [2025/04/22 16:21] (current)
@@ Line 3: / Line 3: @@
 (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//
+<font inherit/inherit;;#e74c3c;;inherit>**Point people/organizers:**</font> //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|https://drive.google.com/drive/folders/1dmAasW0riD3nyfODbQJefdFw1yRK4dpd?usp=sharing]]
+<font inherit/inherit;;#e74c3c;;inherit>**4DN Google Drive folder: **</font> [[https://drive.google.com/drive/folders/1dmAasW0riD3nyfODbQJefdFw1yRK4dpd?usp=sharing|https://drive.google.com/drive/folders/1dmAasW0riD3nyfODbQJefdFw1yRK4dpd?usp=sharing]]
-**4DN Calendar: ** [[https://wiki.4dnucleome.org/4dn:calendar_4dn|https://wiki.4dnucleome.org/4dn:calendar_4dn]]
+**<font inherit/inherit;;#e74c3c;;inherit>4DN Calendar:</font> **  [[https://wiki.4dnucleome.org/4dn:calendar_4dn|https://wiki.4dnucleome.org/4dn:calendar_4dn]]
-**Agenda/Minutes: ** [[https://docs.google.com/document/d/1N8iRYV7cpF60rHMoPW1aaHi11v1_YxluB_0iWNCS0ck/edit?usp=sharing|https://docs.google.com/document/d/1N8iRYV7cpF60rHMoPW1aaHi11v1_YxluB_0iWNCS0ck/edit?usp=sharing]]
+**<font inherit/inherit;;#e74c3c;;inherit>Agenda/Minutes:</font> **  [[https://docs.google.com/document/d/1N8iRYV7cpF60rHMoPW1aaHi11v1_YxluB_0iWNCS0ck/edit?usp=sharing|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|https://docs.google.com/spreadsheets/d/1i3yd_mAioaiFFLOpUkqV0HY0OM0nP1-1jmox4FF-0UY/edit?usp=sharing]]
+**<font inherit/inherit;;#e74c3c;;inherit>Meeting attendee spreadsheet</font>: **  [[https://docs.google.com/spreadsheets/d/1i3yd_mAioaiFFLOpUkqV0HY0OM0nP1-1jmox4FF-0UY/edit?usp=sharing|https://docs.google.com/spreadsheets/d/1i3yd_mAioaiFFLOpUkqV0HY0OM0nP1-1jmox4FF-0UY/edit?usp=sharing]]
-**Email list: ** [[image@4dnucleome.org|]]
+**<font inherit/inherit;;#e74c3c;;inherit>Email list:</font> **  [[image@4dnucleome.org|]]
-**Slack channel:**
+<font inherit/inherit;;#e74c3c;;inherit>**Slack channel: **</font>**#swg-fish-omics-exchange-data-formats**
 ===== Mission Statement =====
@@ Line 21: / Line 21: @@
 [[https://docs.google.com/document/d/1Tu7TySvy0pemS0p1VH2fIwrGFdXEQCGaEeCyKdDjmlA/edit?usp=sharing|Renaming the Merged IOEDF + GSMLDF Subgroup]] (Mission Statement PDF)
-<font inherit/ ;;inherit;;inherit>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.</font>\\ <font inherit/ ;;inherit;;inherit>Central to addressing this hurdle is the work carried out by the **4DN [[https://wiki.4dnucleome.org/4dn:phase2:working_groups:imaging|Imaging Working Group]] (IWG)**  in collaboration with the **[[https://data.4dnucleome.org/help/about/about-dcic|4DN-DCIC]]** , the **[[https://wiki.4dnucleome.org/4dn:phase2:working_groups:integrating_imaging_omics|Imaging and Omics Working Group]] (IOWG)**, and the [[https://www.openmicroscopy.org/|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.</font>
+<font inherit/ ;;inherit;;inherit>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.</font>\\ <font inherit/ ;;inherit;;inherit>Central to addressing this hurdle is the work carried out by the **4DN [[https://wiki.4dnucleome.org/4dn:phase2:working_groups:imaging|Imaging Working Group]] (IWG)**  in collaboration with the **[[https://data.4dnucleome.org/help/about/about-dcic|4DN-DCIC]]**  , the **[[https://wiki.4dnucleome.org/4dn:phase2:working_groups:integrating_imaging_omics|Imaging and Omics Working Group]] (IOWG)**, and the [[https://www.openmicroscopy.org/|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.</font>
 <font inherit/ ;;inherit;;inherit>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.</font>
@@ Line 29: / Line 29: @@
 <font inherit/ ;;inherit;;inherit>We will specifically focus on two initial types of experiments:</font>
-<font inherit/ ;;inherit;;inherit>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|https://doi.org/10.1038/s41596-020-00478-x]]; MINA, [[https://doi.org/10.1038/s41596-021-00518-0|https://doi.org/10.1038/s41596-021-00518-0]]; Hi-M, [[https://doi.org/10.1016/j.molcel.2019.01.011|https://doi.org/10.1016/j.molcel.2019.01.011]]; seqFISH+, [[https://doi.org/10.1038/s41586-019-1049-y|https://doi.org/10.1038/s41586-019-1049-y]]; OligoFISSEQ, [[https://doi.org/10.1038/s41592-020-0890-0|https://doi.org/10.1038/s41592-020-0890-0]]; DNA-MERFISH, [[https://doi.org/10.1016/j.cell.2020.07.032|https://doi.org/10.1016/j.cell.2020.07.032]]; and IGS).</font>
+<font inherit/ ;;inherit;;inherit>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., [[https://doi.org/10.1038/s41596-020-00478-x|ORCA]]; [[https://doi.org/10.1038/s41596-021-00518-0|MINA]]; [[https://doi.org/10.1016/j.molcel.2019.01.011|Hi-M]]; [[https://doi.org/10.1038/s41586-019-1049-y|seqFISH+]]; [[https://doi.org/10.1038/s41592-020-0890-0|OligoFISSEQ]]; [[https://doi.org/10.1016/j.cell.2020.07.032|DNA-MERFISH]]; and [[https://doi.org/10.1126/science.aay3446|IGS]]).</font>
-<font inherit/ ;;inherit;;inherit>2) Single-Molecule Localization Microscopy (SMLM) for volumetric imaging, such as OligoSTORM and OligoDNA-PAINT.</font><font inherit/ ;;inherit;;inherit>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 **[[https://ngff.openmicroscopy.org/latest/|OME-NGFF]]**  format (more specifically** [[https://zenodo.org/record/4113931|OME-Zarr]]**  ) [[https://doi.org/10.1101/2021.03.31.437929|[1]]] and showcase the analysis from the Zarr-file format with software tools like IMGR [2].</font>
+<font inherit/ ;;inherit;;inherit>2)</font>**Single-Molecule Localization Microscopy (SMLM) for volumetric imaging** [[https://doi.org/10.1371/journal.pgen.1007872|[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:
-<font inherit/ ;;inherit;;inherit>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!</font>
+  - Establishment of data models that capture the output of typical OligoSTORM single-molecule localization microscopy (SMLM) data.
+  - Establishment of clear metadata specifications to promote scientific rigor, reproducibility, data exchange, and analysis.
+  - 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 <font inherit/ ;;inherit;;inherit>**[[https://ngff.openmicroscopy.org/latest/|OME-NGFF]]**  format (more specifically **[[https://github.com/ome/ome-zarr-py|OME-Zarr]]**  ) [[https://doi.org/10.1101/2021.03.31.437929|[2]]] and showcase the analysis from the Zarr-file format with software tools like</font>//i//ntegrative //m//odeling of //g//enomic //r//egions (IMGR) <font inherit/ ;;inherit;;inherit>[[https://doi.org/10.1371/journal.pgen.1007872|[1]]].</font>
+It should be noted that this effort will support super-resolved and widefield data being acquired with Bruker <font 11.0pt/";inherit;;inherit>[[https://www.bcm.edu/research/atc-core-labs/integrated-microscopy-core/instrumentation-technology/bruker-vutara-352-storm|Vutara 352]]</font> or [[https://www.bruker.com/en/products-and-solutions/fluorescence-microscopy/super-resolution-microscopes/vutara-vxl.html|Vutara VX]]L microscopes, but welcomes data produced from other imaging platforms!
 ===== 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:
+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:
+  * <font 10pt/Arial;;inherit;;transparent>Please refer to the</font><font 10pt/Arial;;inherit;;transparent>[[https://fish-omics-format.readthedocs.io/en/latest/|ReadTheDocs page]]</font><font 10pt/Arial;;inherit;;transparent>for any and all information about this format and to download example files to get started.</font>
+  * <font 10pt/Arial;;inherit;;transparent>Please report any questions, issues, and proposals for change on the</font><font 10pt/Arial;;inherit;;transparent>[[https://github.com/4dn-dcic/fish_omics_format/issues|GitHub issue page]]</font>
+<font 10pt/Arial;;#ff0000;;inherit>IMPORTANT: All previous GoogleDoc and GoogleSheet representations of FOF-CT are now deprecated and no longer maintained.</font>
+—-
+===== Work in progress =====
+==== FISH Omics Format for Genomic Single Molecule Localization (FOF-GSML) ====
-. [[https://docs.google.com/document/d/1z7rIYsQnbeS7y_SMuwoa8qsWKBD_BpV88vR79WiH_XI/edit?usp=sharing|General description]]
+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:
-. [[https://docs.google.com/spreadsheets/d/1GvqokS5w8Yw2tAngsqDC8YcLdRha5cGr/edit?usp=sharing&ouid=101141664079197066125&rtpof=true&sd=true|Specifications]]
+  - [[https://docs.google.com/presentation/d/15NYN3ZQFEzFEZrUTX0obSP-XEjsJ84MM/edit?usp=sharing&ouid=101141664079197066125&rtpof=true&sd=true|FOF Data Model]]
 ----

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