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Feature #4973

open

Upload Helios images to appion

Added by William Rice over 7 years ago. Updated over 5 years ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
05/17/2017
Due date:
% Done:

0%

Estimated time:

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

Files

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semheader.py (2.5 KB) semheader.py python script for reading helios image header information William Rice, 05/17/2017 02:14 PM
SEM_upload.py (947 Bytes) SEM_upload.py Sargis Dallakyan, 02/20/2019 06:13 PM
uploadSEM.sh (703 Bytes) uploadSEM.sh Sargis Dallakyan, 02/20/2019 06:13 PM

Related issues 1 (1 open — 0 closed)

Related to Appion - Feature #5464: Helios integration with Appion pipelineNew01/24/2018

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 #1

Updated by Sargis Dallakyan about 7 years ago

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.

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 #2

Updated by Sargis Dallakyan about 7 years ago

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

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 #3

Updated by Sargis Dallakyan over 6 years ago

  • Related to Feature #5464: Helios integration with Appion pipeline added
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 #4

Updated by Sargis Dallakyan over 5 years ago

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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