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4dn:phase2:working_groups:imaging:fish_omics_exchange_data_formats
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4dn:phase2:working_groups:imaging:fish_omics_exchange_data_formats [2021/11/22 11:43] caterina_str |
4dn:phase2:working_groups:imaging:fish_omics_exchange_data_formats [2025/04/22 16:21] (current) |
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| - Establishment of data models that capture the output of typical OligoSTORM single-molecule localization microscopy (SMLM) data. | - 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 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://zenodo.org/record/4113931|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> | + | - 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! | 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! | ||
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| ==== FISH Omics Format for Chromating Tracing (FOF-CT) ==== | ==== 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: |
| - | - [[https://docs.google.com/document/d/1z7rIYsQnbeS7y_SMuwoa8qsWKBD_BpV88vR79WiH_XI/edit?usp=sharing|General description]] | + | * <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> |
| - | - [[https://docs.google.com/spreadsheets/d/1GvqokS5w8Yw2tAngsqDC8YcLdRha5cGr/edit?usp=sharing&ouid=101141664079197066125&rtpof=true&sd=true|Specifications/user-guide]] | + | * <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> |
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| + | <font 10pt/Arial;;#ff0000;;inherit>IMPORTANT: All previous GoogleDoc and GoogleSheet representations of FOF-CT are now deprecated and no longer maintained.</font> | ||
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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: | 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/presentation/d/1PXcWT1uPEb5W5QAh6-QKZyxfnieiffA53f5qu6qsrMU/edit?usp=sharing|FOF Data Model]] | + | - [[https://docs.google.com/presentation/d/15NYN3ZQFEzFEZrUTX0obSP-XEjsJ84MM/edit?usp=sharing&ouid=101141664079197066125&rtpof=true&sd=true|FOF Data Model]] |
| - | - [[https://docs.google.com/document/d/1SwGB5VWploc9zATHg25kWGkA0g5eQvdFmyhjS_-eE28/edit?usp=sharing|FOF-GSML draft specifications]] | + | |
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4dn/phase2/working_groups/imaging/fish_omics_exchange_data_formats.1637610200.txt.gz · Last modified: 2025/04/22 16:21 (external edit)