imextract_init fails for CV7000 data with multiple "timelines"

[scottberry]

imextract_init fails when preprocessing 378 tifs from CellVoyager. See screenshot for details. Image details: 3 channels, single image tifs from 96-well plate 9 sites per well. Data is available for testing at 172.23.67.79/data/Data/Users/Scott/20170106-EU-CT-opt-Scott I also tried to resubmit this data as a 384-well plate, however the result was the same.

[scottberry]

This may be related to having multiple "timelines" in the Yokogawa acquisition for this plate. i.e. some wells in the plate have different numbers of acquisition channels. I successfully uploaded and preprocessed/created pyramids for two wells of this plate which have the same number of aquisition channels, without providing the metadata files. This is however broken (at metaconfig) if I provide the metadata files.

[hackermd]

What's the name of the experiment? I will have a look.

[scottberry]

Image details: 3 channels, single image tifs from 96-well plate 9 sites per well. Data is available for testing at 172.23.67.79/data/Data/Users/Scott/20170106-EU-CT-opt-Scott I also tried to resubmit this data as a 384-well plate, however the result was the same.

[hackermd]

Can you please add one of my public keys to ~/.ssh/authorized_keys to provide me access to your machine. You can get the keys from Github:

wget -O - https://api.github.com/users/hackermd/keys

[scottberry]

Which machine? My local machine? Why do you need this?

The data is all on sciencecloud storage and I am doing uploads from instances launched from sciencecloud instance snapshot tm_client

Is there some issue with permissions on the data? I could change this on science-cloud storage, if required?

Scott

On 10 Feb 2017, at 10:15, Markus D. Herrmann notifications@github.com wrote:

Can you please add one of my public keys to ~/.ssh/authorized_keys to provide me access to your machine. You can get the keys from Github:

wget -O - https://api.github.com/users/hackermd/keys — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/pelkmanslab/TissueMAPS/issues/2#issuecomment-278894466, or mute the thread https://github.com/notifications/unsubscribe-auth/AFKEaLsx_nCGFJxpagawNDK-cwroE0-Oks5rbCqsgaJpZM4Lgu5f.

[hackermd]

I was referring to machine 172.23.67.79. Ok, got it - its the new storage server, so I can mount it..

[scottberry]

Yes, it would be nice to give the new storage a name.

On 10 Feb 2017, at 10:29, Markus D. Herrmann notifications@github.com wrote:

I was referring to machine 172.23.67.79. Ok, got it - its the new storage server, so I can mount it..

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[hackermd]

@alecrimi I agree it would be nice to give it a domain name similar to the already existing sciencecloudstorage.pelkmanslab.org/pelkmanslab-share-1`

[scottberry]

@alecrimi perhaps best to wait until the storage is partitioned (next week?) and give a nice new series of names to the different partitions

On 10 Feb 2017, at 10:34, Markus D. Herrmann notifications@github.com wrote:

@alecrimi https://github.com/alecrimi I agree it would be nice to give it a domain name similar to the already existing sciencecloudstorage.pelkmanslab.org/pelkmanslab-share-1`

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[hackermd]

Some inspiration: cities of Games of Thrones :)

[scottberry]

@alecrimi, very good.

On 10 Feb 2017, at 10:41, Markus D. Herrmann notifications@github.com wrote:

Some inspiration: cities of Games of Thrones http://gameofthrones.net/world-of-westeros/37-cities.html :)

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