https://github.com/biop/ijp-operetta-importer
PerkinElmer Operetta Importer using BioFormats!
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.0%) to scientific vocabulary
Repository
PerkinElmer Operetta Importer using BioFormats!
Basic Info
Statistics
- Stars: 9
- Watchers: 3
- Forks: 3
- Open Issues: 10
- Releases: 0
Metadata Files
README.md
PerkinElmer/Revvity Operetta Importer Command and API
Features
This repo has a clear(ish) API and a nice SciJava InteractiveCommand
Documentation
We are hosting the JavaDoc as GitHub pages at https://biop.github.io/ijp-operetta-importer/
The main class you should focus your attention on is OperettaManager
If you'd like to see some examples on how it can be used, please check the Scripts folder. This contains a few Groovy examples on how to call the Operetta Importer API
Installation in Fiji
Go to Help > Update...
Click Manage Update Sites
Activate the PTBIOP update site.
Usage
Go under Plugins -> BIOP -> Operetta importer -> Operetta importer or type Operetta importer in the search bar.
Select input folder
- Select the folder to analyse. It should contain all individual images, WITH the
index.idx.xmlfile. - Click on
Ok
Select data to analyze
- Click on
Choose Wellsbutton to select a subset of available wells. - Click on
Choose Fieldsbutton to select a subset of available fields. - Click on
Preview Well slicebutton to get a preview of the data - Write down a subset of channels to analyze
- Write down a subset of slices to analyze
- Write down a subset of frames to analyze
Select processing options
- Choose a downsample factor. BE CAREFUL: DO NOT SELECT 0. If you don't want to do any downsampling, select a downsampling of 1.
- Check the box if you want to average pixels during downsampling.
- Select a fusion option
- Do not fuse fields
- Fuse with stage coordinates => put fields next ot the other without doing any blending
- Fuse using Grid/Collection stitching => correctly stitch fields with affine transforms
- Select a flipping option
- Do not flip
- Flip horizontal
- Flip vertical
- Flip both
- Select a projection option
- No Projection
- mean
- min
- max
- median
- std
- sum
- Select the min/max values of the intensities
Output and Saving
- Choose a directory where to save the output images
- Check the box to save the fused images as OME-TIFF and to generate the corresponding companion.ome file. This option only works if you have fused fields together.
- A message is written at the bottom of the UI to inform you on the size and time the analysis will take. Finally, you can click on
Process.
Owner
- Name: BioImaging And Optics Platform (BIOP)
- Login: BIOP
- Kind: organization
- Location: Lausanne, Switzerland
- Website: https://biop.epfl.ch
- Repositories: 84
- Profile: https://github.com/BIOP
All the code that is publicly available/published by the BioImaging And Optics Platform (BIOP)
GitHub Events
Total
- Issues event: 8
- Delete event: 2
- Issue comment event: 10
- Push event: 19
- Pull request review comment event: 16
- Pull request review event: 8
- Pull request event: 4
- Gollum event: 3
- Create event: 6
Last Year
- Issues event: 8
- Delete event: 2
- Issue comment event: 10
- Push event: 19
- Pull request review comment event: 16
- Pull request review event: 8
- Pull request event: 4
- Gollum event: 3
- Create event: 6
Dependencies
- actions/checkout v2 composite
- actions/setup-java v3 composite
- actions/checkout v2 composite
- actions/setup-java v3 composite
- net.imagej:imagej
- net.imagej:imagej-legacy
- ome:formats-gpl
- org.codehaus.groovy:groovy
- org.slf4j:slf4j-api
- org.slf4j:slf4j-log4j12 1.7.5 test