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2 Color Correction
robertprior-fixstars edited this page Sep 25, 2019
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The color correction stage downsamples and color corrects the input images. It is important to note that this stage requires exactly 4 color channels in the input. In the input directory, the downsampled files will be created with
-downsample
added between the file based name and the round number string.
The downsampled files are then further used in color correction. In the color correction folder, each round will have the shifted images created with names determined by the parameter:
params.SHIFT_CHAN_STRS
The first channel will be a symlink directing to the file with the same name in the input folder. Additionally a file colorcals.mat will be created for each round which contains a chan_offsets, 4x3 matrix with the shifts for the round.
- 1 Setup Cluster
- 2 Color Correction
- 3 Normalization
- 4 Registration
- 5 Puncta Extraction
- 6 Base Calling
- Performance Profile
- Example Batching
- Summary Reporting (link to page) / Analysis (link to page) All of above would be bullet points but thought each folder with useful scripts in the repository would have its own page with example usages and descriptions for the files under the given directory. Unsure on this as haven't used anything under these directories directly myself (i.e not through runPipeline) apart from tests/perf-profile/summarize-stat-logs.sh. Should any of these have a separate page? Note have not made pages for this yet as not sure how many should be made or if this break down makes sense.
- Troubleshooting