Feature #4973
open
Upload Helios images to appion
Added by William Rice over 7 years ago.
Updated over 5 years ago.
Description
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:
* Convert all tiff images into a single mrc stack (Imod tools)
* determine alignment parameters (Imod tools)
* Align (Imod tools)
* fix intensity gradients (ImageJ)
* import into Amira for rescaling to cubic voxels, segmentation
My script for heading the header of the tiff tiles is attached
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Related issues
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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
- Related to Feature #5464: Helios integration with Appion pipeline added
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
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