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5 Puncta Extraction
The puncta extraction stage attempts to find puncta in the registered images. All rounds are combined into a basename_allSummedNorm file created in the puncta extraction dir. Puncta are attempted to be found in this combined image with a combination of thresholding to remove background and watershed to find potential puncta regions. These candidate regions are judged to be puncta based on the params.PUNCAT_SIZE_THRESHOLD and params.PUNCTA_SIZE_MAX in the loadParameters.m . An image visually showing the found puncta is created in a file marked basename_allSummedNorm_puncta.
Two mat files are also created basename_centroids+pixels and basename_punctavoxels. The basename_centroids+pixels.mat contains a puncta_centroids matrix with a row per puncta containing the X,Y,Z co-ordinates of the found puncta. A puncta_voxels matrix also contains a cell array per puncta describing the shape of the found puncta.
The basename_punctavoxels.mat contains two variables puncta_set_cell and puncta_indices which contain additional information for the found 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