sorgerlab/o2-deployment

Name: o2-deployment

Owner: sorgerlab

Description: Deployment of lmod modules and underpinning software on O2

Created: 2017-11-03 15:56:31.0

Updated: 2017-11-09 19:53:08.0

Pushed: 2017-11-15 20:56:07.0

Homepage: null

Size: 6

Language: Python

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README

O2 Deployment of useful modules and tools

Modules

Several additional modules for O2 are available.

• ashlar
• stitcher
• omero-scripts

Install Instructions

Making use of these modules requires adding the path to the custom modules to your MODULEPATH on O2. This can be accomplished easily by adding the following line to your ~/.bashrc on O2.

rt MODULEPATH=$MODULEPATH:/n/groups/lsp/o2/modulefiles

After adding this (and starting a new shell), modules will be permanently available in your O2 account.

Example Usage in CycIF

Load and use the ashlar and stitcher modules to stitch and register CycIF images and then generate pyramids as an OME-tiff, ready for import to OMERO.

1. Obtain flat-field images by imaging specially-prepared slides or using the CIDRE algorithm on existing datasets (tools forthcoming).
2. Use mosaic command from ASHLAR to stitch and register images.
3. Use stitcher command from Glencoe Software's stitcher to generate pyramids.
4. Import pyramid into OMERO.

Steps 2 and 3:

ad the ashlar and stitcher modules
le load ashlar stitcher

e mosaic to stitch and register the images in the given `scan_path`.
ic <scan_path> [--ffc <flat_field_path>]

eate pyramids for the given `./scan*` directory and output as
ataset-name`.tif, merging the channels into one file.
cher create_pyramid --input ./scan* --output <dataset_name>.tif \
mergeChannels

ean up (logging out will also accomplish this)
le unload ashlar stitcher

Step 3

ad the omero module
le load omero

port a file or (recursively) a directory
o import <file_or_dir>

ean up (logging out will also accomplish this)
le unload omero