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)
*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
Metadata documents, October 2017:
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:
Groudine G4 TetO gene trap library
NUP107 A647 images:
Ries/Ellenberg, EMBL
Ritland/Groudine, FredHutch
Singer Lab, Einstein and Janelia
Bewersdorf Lab, Yale
Zipfel, Cornell
Peltier/Ellisman
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.