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Upload Helios images to appion #4973

Open leginonbot opened 4 months ago

leginonbot commented 4 months ago

Author Name: William Rice (@wjrice) Original Redmine Issue: 4973, https://emg.nysbc.org/redmine/issues/4973 Original Date: 2017-05-17

I would like to be able to upload Helios images to appion. Eventually to be able to do all of our fib-sem processing in the Appion workflow. Current workflow:

My script for heading the header of the tiff tiles is attached

leginonbot commented 4 months ago

Original Redmine Comment Author Name: Sargis Dallakyan (@dallakyan) Original Date: 2017-08-10T21:46:55Z

Found FIB SEM image data set of Caenorhabditis elegans exposed to 60 nm Au nanoparticles at: https://catalog.data.gov/dataset/fib-sem-image-data-set-of-caenorhabditis-elegans-exposed-to-60-nm-au-nanoparticles

I put some thoughts on this and we will need to decide where this metadata will be stored in our database. In the meantime I have been looking into https://www.openmicroscopy.org/omero/

I've installed this and imported one of the C elegans datasets at http://192.168.4.29:4080. I like that OMERO.web is using Django and it has very nice looking user interface. I can send username/password in an email if interested. I plan to demo this during the hackathon.

leginonbot commented 4 months ago

Original Redmine Comment Author Name: Sargis Dallakyan (@dallakyan) Original Date: 2017-08-17T14:04:10Z

Created appion/bin/uploadFIB-SEMImages.py to upload tif images. An example session is at http://emgweb.nysbc.org/betamyamiweb/imageviewer.php?expId=4709

Usage: uploadFIB-SEMImages.py [options]
Options:
  -h, --help            show this help message and exit
 ...
  --image-dir=DIR       Directory that contains TIF files to upload
  --projectid=projectID ID of the project to upload images to
  --session-name=SESSIONNAME
                        Session name, e.g., 17aug06a. If provided append
                        images to this session.
Example:
uploadFIB-SEMImages.py --image-dir=/gpfs/leginon/sargis/workspace/FIBSEM-Celegans-tiff-set1-106/ --description='test' --projectid=364 --session-name=17aug16l34
leginonbot commented 4 months ago

Original Redmine Comment Author Name: Sargis Dallakyan (@dallakyan) Original Date: 2019-02-20T23:19:48Z

Adding scripts used to upload images. This script is run every 10 minutes on node01:

[root@node01 bin]# more /var/spool/cron/root
0/10 * * * *  bash -l /root/bin/uploadSEM.sh

It looks for a file named upload.cfg and modified withing last 3 days. An example for upload.cfg:

[sem]
project=211
z-slice=5
description=Testing SEM upload