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Stage Overview
robertprior-fixstars edited this page Sep 25, 2019
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The ExSequence pipeline consists of the following stages:
| Stage | Description |
|---|---|
| 1 Setup Cluster | prepares for running MATLAB parallel processing. |
| 2 Color Correction | does downsampling and tries to normalize across color channels. |
| 3 Normalization | does some normalization within rounds. |
| 4 Registration | registers rounds to a reference round |
| 5 Punta Extraction | tries to find puncta in the normalized and combined images. |
| 6 Base Calling | uses a ground truth dictionary, a list of expected types of puncta, to reduce the number of found puncta in the previous step. Additionally, this step labels the extracted puncta. |
- 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