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--- 4dn:phase2:working_groups:imaging [2021/02/15 13:07]
caterina_str
+++ 4dn:phase2:working_groups:imaging [2025/04/22 16:21] (current)
@@ Line 23: / Line 23: @@
 <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>2) As a coordination platform to initiate sub-groups (SWG) that focuses on concrete barriers related to imaging within 4DN, as a discussion forum about solutions and as a place for such SWG to report the outcome of their work before implementing policies via the DCIC. Subgroups can have any format, should be led by their initiators, and typically aim to solve problems (or define clear strategies for the resolution of more complex problems) on a short time scale of 3-6 months. The IWG encourages all 4DN members to initiate SWGs based on their interests and needs. SWG should explicitly be open to being initiated by postdocs and staff scientists.</font>
-<font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>**Active SWGs: **</font>
+==== Microscopy Metadata is essential for reporting and reproducibility in microscopy ====
+=== Major Achievements: ===
+Work from IWG has been featured in a FOCUS issue on Nature Methods in December 2021
+  * Reporting and Reproducibility in Microscopy –> [[https://www.nature.com/collections/djiciihhjh|FOCUS ISSUE]]
+  * Community-driven 4DN-BINA-OME [[https://doi.org/10.1038/s41592-021-01327-9|Microscopy Metadata Specifications]]
+  * [[https://doi.org/10.1038/s41592-021-01315-z|Micro-Meta App]] tool for collecting Microscopy Metadata (now in use on the [[https://data.4dnucleome.org/tools/micro-meta-app|4DN Data]][[https://data.4dnucleome.org/tools/micro-meta-app| Portal]])
+==== Exchange data formats for imaging experiments ====
+<font 11pt/Arial;;#000000;;inherit>The purpose of this work is to develop a standard format to allow the exchange of imaging results and encourage the development of shared analysis, modeling and visualization pipelines.</font><font 11pt/Arial;;#000000;;inherit>Currently, we are working on two formats to exchange FISH Omics results.</font>
+  - FISH omics Format for Chromatin Tracing (FOF-CT) is released and provisionally approved by the SC (see below)
+  - FISH omics Format for Genomic Single Molecule Localization is in progress and current status can be found at the bottom of the exchange data format subgroup [[https://wiki.4dnucleome.org/4dn:phase2:working_groups:imaging:fish_omics_exchange_data_formats|page]].
+=== FISH omics Format for Chromatin 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 on 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;;inherit;;transparent>Please refer to this example dataset that was deposited on the 4DN-Data Portal</font><font 11pt/Arial;;#000000;;inherit>using FOF-CT:</font> * <font 11pt/Arial;;#000000;;inherit>Liu M, Lu Y, et al.,</font><font 11pt/Arial;;#000000;;inherit>Nature communications</font><font 11pt/Arial;;#000000;;inherit>2020 →</font><font 11pt/Arial;;#1155cc;;inherit>[[https://data.4dnucleome.org/experiment-set-replicates/4DNESXYFBZMI/|https://data.4dnucleome.org/experiment-set-replicates/4DNESXYFBZMI/]]</font>
+<font 10pt/Arial;;#ff0000;;inherit>IMPORTANT: All previous GoogleDoc and GoogleSheet representations of FOF-CT are now deprecated and no longer maintained.</font>
+===== Active SWGs: =====
   - <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>**SWG Image Data Documentation and Submission**:__ Lead__: Andrea Cosolo, Andrew Schroeder, and Caterina Strambio De Castillia (alphabetic order). __Mission Statement:__</font>The aim of this SWG is to improve awareness of 4DN members of the tools and procedures made available by the DCIC for image data documentation, hold appropriate training sessions and encourage rapid and stringent data submission.
@@ Line 35: / Line 66: @@
 <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit><font inherit/inherit;;#c0392b;;inherit>**Next meeting: 3/2/2021 **</font></font>
+=====  =====
 ===== Closely Connected Interest and Working Groups =====
@@ Line 78: / Line 111: @@
 <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>To exchange quantitative results from imaging experiments, the 4DN-Ph1 IWG developed [[https://data.4dnucleome.org/resources/experimental-resources/imaging_file_formats|three data exchange formats]] that are currently utilized by the DCIC and could be applicable for Ph2:</font>
-  - <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>[[https://elasticbeanstalk-fourfront-webprod-blobs.s3.amazonaws.com/ab4e93c7-c9c6-4e4e-8eea-4c77464c3354?response-content-disposition=inline%3B%20filename%3D4DN_DNA_FISH_format_DRAFT.pdf&AWSAccessKeyId=AKIAZLS5EJLSO75TQUDX&Signature=nhtjD%2B8h6ccGxH1xktW6D1TneAc%3D&Expires=1611919756|DNA FISH Spot Localization _v01]] (Draft),</font>
+  - <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>[[https://elasticbeanstalk-fourfront-webprod-blobs.s3.amazonaws.com/ab4e93c7-c9c6-4e4e-8eea-4c77464c3354?response-content-disposition=inline%3B%20filename%3D4DN_DNA_FISH_format_DRAFT.pdf&AWSAccessKeyId=AKIAZLS5EJLSO75TQUDX&Signature=4au5BAct8Pf1DhTkRcNd2OkTcTw%3D&Expires=1613552572|DNA FISH Spot Localization _v01]] (Draft),</font>
-  - <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>[[https://elasticbeanstalk-fourfront-webprod-blobs.s3.amazonaws.com/fafc1e95-396a-4140-8168-7a9cdc8aabcf?response-content-disposition=inline%3B%20filename%3D4DN_DNA_SEGMENTATION_format_DRAFT.pdf&AWSAccessKeyId=AKIAZLS5EJLSO75TQUDX&Signature=OzlTcnr02H6M1skBAxCYcMmvFoA%3D&Expires=1611919782|Segmentation _v01]] (Draft), and</font>
+  - <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>[[https://elasticbeanstalk-fourfront-webprod-blobs.s3.amazonaws.com/fafc1e95-396a-4140-8168-7a9cdc8aabcf?response-content-disposition=inline%3B%20filename%3D4DN_DNA_SEGMENTATION_format_DRAFT.pdf&AWSAccessKeyId=AKIAZLS5EJLSO75TQUDX&Signature=RZWkdmk6zWPxPwWfSX%2Bb4KGX55M%3D&Expires=1613552547|Segmentation _v01]] (Draft), and</font>
-  - <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>[[https://elasticbeanstalk-fourfront-webprod-blobs.s3.amazonaws.com/030701ac-3e21-4cae-b4bf-0ca67949c397?response-content-disposition=inline%3B%20filename%3D4DN_SPT_format.pdf&AWSAccessKeyId=AKIAZLS5EJLSO75TQUDX&Signature=dAhYMofWuMIvk%2FAWeNU515SERdM%3D&Expires=1611919805|Single Particle Tracking]] (Approved by Phase I IWG)</font>
+  - <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>[[https://elasticbeanstalk-fourfront-webprod-blobs.s3.amazonaws.com/030701ac-3e21-4cae-b4bf-0ca67949c397?response-content-disposition=inline%3B%20filename%3D4DN_SPT_format.pdf&AWSAccessKeyId=AKIAZLS5EJLSO75TQUDX&Signature=iYgdigy%2FJm%2FdPmNdwE4NTumRASA%3D&Expires=1613552499|Single Particle Tracking]] (Approved by Phase I IWG)</font>
 <font inherit/Arial,Helvetica,sans-serif;;inherit;;inherit>These data exchange standards are extremely relevant for Phase 2 and could serve as a great starting point for further development. In addition, it is important to note that as part of the effort to develop a [[https://ngff.openmicroscopy.org/latest/#intro|Next-Generation File Format for image data]], the OME consortium is developing standards for recording Region of Interests (ROI), spots, and trajectories which is extremely relevant to this topic.</font>

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