The mailing list for the working group has been changed. Please use image@4dnucleome.org from now on as the new mailing list address.

IMAGING DATA STANDARDS: ESTABLISH STANDARDS FOR DATA FORMATS AND QUALITY CONTROL

Co-Chairs:

Year 4: Rob Singer and David Grunwald

Year 3: Rob Singer, Joan Ritland and David Grunwald

Year 2: Rob Singer, Joan Ritland .

Year 1: Mark Ellisman, Xavier Darzacq

DATA UPLOAD IS LIVE

(Since March, 2018)

Upload of imaging data to the 4DN portal is live. Please let us know if you have Imaging data gathered with 4DN funding and you are not on this list:https-3A__docs.google.com_spreadsheets_d_14Msheyhc-2Du8KnU3R5W8Ow-2DuSPyoMKlWBsvJYAsRTxVg_edit-3Fusp-3Dsharing.

This link gives information on the upload process from DCIC:180306_dcic_data_upload.pdf

1st Monday of every month, 12:00 pm PT (3:00 pm ET)
Meeting Link:
https://4dnucleome.webex.com/4dnucleome/j.php?MTID=m033f3efc842cb3821d91cfbf9a125375
Meeting number: 806 955 362
Meeting password: KvTsi3bA
Host key: 927479
Audio Connection: 1-415-655-0002 US TOLL
Access code: 806 955 362

WEBEX EMERGENCY CONTACT INFORMATION:

KATE RIVERA

858-822-1626 (OFFICE)

• Develop and distribute calibration tool to imaging groups and get feedback.
• Benchmark imaging to standardize among groups and imaging platforms in collaboration with the Joint Analysis WG.
• Develop a workflow to process, analyze and store imaging data.
• Compare methods and develop an SOP for high resolution FISH.

• Distribute common calibration sample, evaluate images of sample from different imaging platforms. Ellenberg Common Imaging Sample Nup U2OS
• Identify a second Tier 1 cell line that imagers as well as omics folks will use. November meeting recommends IMR-90 for consideration. April meeting recommends the inbred mESC line, JM8.N4 for consideration. Both lines approved by Cell Lines WG.
• Develop metadata standards for production labs. Imaging WG members David Baddeley and David Scalzo working with DCIC on this goal. See May 2017 lock-in meeting summary below, and Guidance to DNA FISH labs.docx.

*SCOPE* The 4D Nucleome Initiative investigators efforts will result in production of a variety of different types of datasets obtained by imaging the nuclei of single cells with multiple methodologies. An immediate objective of this working group is to identify the image data types; to develop a format for each and to keep a working list of the nature of these datasets. The group will discuss these topics and determine our course of action. We hope to determine how these data would be archived and retrieved by other 4DN groups, and the larger community of biomedical investigators. We will also work to implement, among the imaging groups of the 4D nucleome, practices that enable a suitable data sharing strategy – one that might resemble that of the genomics field (eg., data deposition prior to publication and shared upon publication). *TASKS* Our first task will be to define the list of datasets and data types that are being generated under 4DN support and assemble a small working group with sufficient expertise to work out the details required to properly annotate and archive all of them. After our meeting we will collect information about these datasets from the different groups.

- For each type of data we consider how to establish bridges that link to data types of the other working groups

• - Determine Publication policy (set standards for data release upon publication)
• - Connect the imaging data to emerging “Omics” data standards ((discuss where the data will be stored, unify metadata, [eg., discuss agreements regarding minimal metadata required for each data type])
• - Consider tools available for data analysis [eg., discuss examples of tools available or under development and look into and/or integrate data within and between image data types; potentially to connect these data to omics-oriented data resources].
• - Consider discussions of specific cell lines and samples types (compatibility with the metadata standards efforts)

1. February 2016FEB MEETING NOTES
2. March 2016March agendaMARCH MEETING NOTES
3. April 2016 -APRIL MEETING NOTES
4. May 2016MAY MEETING NOTES
5. June 2016JUNE MEETING NOTES
6. July 2016JULY MEETING NOTES
7. September 2016SEPTEMBER MEETING NOTES
8. November 2016November meeting notes
9. December 2016December 2016 meeting notes
10. January 2017January 2017 minutes
11. February 2017Feb 2017 minutes
12. March 2017:DCIC updates, March 2017 minutes
13. April 2017:April 2017 meeting notes
14. May 2017May 2017 minutes
15. Lock-in May 2017 SummaryWorcester Calibration Standards/Metadata Meeting Summary
16. June 2017 minutesJune 2017 minutes
17. July 2017 minutesJuly 2017 minutes
18. August 2017 minutesAugust Imaging Minutes.docx
19. Sept 2017 minutes
20. October 2017 minutes
21. November 2017 minutes: Jason Swedlow presentation on Euro BioImaging image curation pipelines
22. January 2018 minutes : LINCspresentation on image curation and integration with other data types
23. No Feb meeting
24. March 6, 2018.DCIC and Gianluca Pegora presentation on progress with Misteli HIP FISH data upload. (minutes, recordings)
25. March 21, 2018.Allen Institute for Cell Sciences presented their approaches to image data management and machine learning for predicting nuclear structure. (minutes,recordings)
26. April 3, 2018 Anders Hansen (Darzacq lab) presented their SPT data and progress on SPT data annotation and upload. IWG approves upload of trajectory data only at this time - raw and analyzed data formats will be defined in the future. Caterina Strombio, a non-4DN member who has been designing tools for managing and analyzing SPT data at UMASS, sat in on this call. (recordings, Anders Hansen SPT format ppt, minutes)
27. April 18, 2018. Charles Kenworthy (Coleman/Singer) presentedSPTdatafrom theirnew BioRxivpaper. Kenworthy ppt. Kenworthy movie. The SPT metadata format presented at the April 3rd meeting was approved . There were no commentson the drafts Anders circulated. Caterina Strombio sat in onthis call also. (recordings, minutes)
28. May 1,2018Tristin Liu (Ren lab) presents SOX2 imaging data. This is one of the joint analysis common gene targets (recordings,minutes)
29. May 16, 2018.Sofi Quinodoz (Guttman Lab) will present imaging data from their SPRITE paper (recordings)
30. June 5, 2018 Organizational MeetingJune 4, 2018 minutes
31. June 20, 2018 Raja Ghosh (Liphardt lab) presents SPT data and progress on SPT data annotation and upload.(recording)
32. August 8 at 1PM Pacific - note time change - David Baddeley will present approaches to image curation.(recording)
33. September 4, 2018 - (recording), agenda
34. September 19, 2018. Peter Wang (presenter), AGENDA, Recording, Minutes,
35. October 2, 2018 - Dr. Bing Ren, Dr. William Noble and Dr. Susanne Rafelski will present. (recording)
36. October 17, 2018 - Ting Wu (presenter), (PP presentation), (recording)
37. November 6, 2018 - Paul Kaufman and Gianluca Pegoraro (presenters - 20 minutes shorter), talk discussion (20 minutes), Subgroup Omics to Imaging report (20 minutes), AGENDA, (recording)
38. November 28, 2018 - (recording)
39. December 19, 2018 - (recording)
40. January 16, 2019 - CANCELLED
41. February 4 , 2019 - (recording)
42. March 4, 2019 - (recording), Protocol for March 4th IWG meeting,
43. April 1, 2019 - agenda, recording, protocol for April 1st IWG meeting
44. May 6, 2019 - agenda, recording
45. June 3, 2019 - CANCELLED
46. July 1, 2019 - agenda - CANCELLED
47. August 5, 2019 - agenda, recording
48. September 9, 2019 - CANCELLED
49. October 7, 2019 - recording
50. November 4, 2019 - slides, recording (Talk by Max Huisman (Grunwald lab) MetaMax Generation 3 – What you would like to know about your microscope that will stay hidden from meta data), recording
51. December 2, 2019 - CANCELLED
52. January 6, 2020 - CANCELLED
53. February 3, 2020 - recording
54. March 2, 2020 - CANCELLED
55. April 6, 2020 - CANCELLED
56. May 4, 2020 - Agenda, Recording link
57. June 1, 2020 - Agenda, Recording link

• Imaging group 2017 Annual Report
• Imaging Group Working Dinner September 19, 2017 Raw Notes
• Microscopy Calibration Demo

Metadata documents, October 2017:

• PSF protocol
• Metadata

Guidance for uploading DNA FISH data to DCIC Guidance to DNA FISH labs.docx

Open the docs below with Google docs to be able to add your comments:

• Technical specifications for LSM calibration
• Ellenberg Common Imaging Sample Nup U2OS
• Technical specifications for wide field calibration-3

Groudine G4 TetO gene trap library

Groudine G4 TetO gene trap library

NUP107 A647 images:

Ries/Ellenberg, EMBL

• Staining Protocol
• Ries_Airyscan_1
• Ries_Airyscan_2
• STORM

Ritland/Groudine, FredHutch

• Ritland_Raw_Airyscan
• Ritland_processed_Airyscan
• Ritland_airyscan_metadata
• Ritland_imaging text summary
• Ritland_Widefield stack_dark
• Ritland_Widefield stack_647
• Ritland_widefield_metadata

Singer Lab, Einstein and Janelia

• Singer SIM
• Singer widefield
• Singer_lab_JRC.zip

Bewersdorf Lab, Yale

• Bewersdorf LeicaSP8 text
• Bewersdorf LeicaSP8

Zipfel, Cornell

• Zipfel_NUP_Images_slide1.zip
• Notes_WZipfel_NUP_images.pdf

Peltier/Ellisman

• Ellisman LeicaSPEII
• Ellisman_OlympusFluoview1000

Insert spreadsheet members

The mailing list to use for communication in this Working Group is image@4dnucleome.org. Emails sent there will go to everyone on the list. Replying to an email from the list will also send it to everyone in the list.