Uploading Image Files to IDR and BBBC

[gwaybio]

Uploading the images into the public domain is a very important part of the research process. I will upload image files to the Image Data Resource and add URL and metadata information to the Broad Bioimage Benchmark Collection.

We will use this issue to outline the required steps. First, I will need to restore the image files from aws glacier storage. @shntnu - can you link the most recent resources?

---

edit

data how available: https://idr.openmicroscopy.org/webclient/?show=screen-2701

[hkhawar]

@Gregory Way gway@broadinstitute.org Thanks alot. I will start working on it tomorrow

On Wed, Sep 2, 2020 at 4:50 PM Greg Way notifications@github.com wrote:

turns out that we actually have 17,285 illum corrected files missing.

1,920 "f09" files missing per plate 9 plates 5 "f01" files missing only in plate SQ00014610 1,920 * 9 + 5 = 17,285

Transfer files into a new folder again?

Yup that would be a great help. Let me know once they are done.

I have confirmed that all of these files are now in a separate folder. The folder is /home/ubuntu/bucket/projects/2015_07_01_Cell_Health_Vazquez_Cancer_Broad/tmp_version_three .

Note that the subfolder is tmp_version_three.

@hkhawar https://github.com/hkhawar all set for the next (and hopefully final!) iteration of the illum correction pipeline. Thanks again

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/cell-health/issues/106#issuecomment-686047898, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIUGCWNEWSRLCBOYJWHV5FTSD243JANCNFSM4K3RAT7Q .

[gwaybio]

I have confirmed that all 17,285 files have been corrected, and that they are all the same size:

size	n	frac
9348718	17285	1

I will work on uploading them directly to IDR now (they gave us an FTP)

[hkhawar]

@gwaygenomics great

[gwaybio]

images are now public: https://idr.openmicroscopy.org/webclient/?show=screen-2701