Change .format to % in dataset.py#69
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LesikDee wants to merge 82 commits intoemanuega:v0.2.0from
LesikDee:LesikDee-dataset-format
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Change .format to % in dataset.py#69LesikDee wants to merge 82 commits intoemanuega:v0.2.0from LesikDee:LesikDee-dataset-format
LesikDee wants to merge 82 commits intoemanuega:v0.2.0from
LesikDee:LesikDee-dataset-format
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…n of parallel analysis tasks
* updated _run_analysis so GenerateAdaptiveThreshold (GAT) does not crash if the task is reran after a crash. The problem occurs only if the GAT folder is not deleted prior to a rerun. In that case, merlin would see that the .npy files exist so blankCounts would not be initialized. Merlin would crash when blankCounts += is called, because is trying to sum None and a matrix
Updated aws bucket name.
…an be restarted more quickly.
Small modifications to code/analysis organization
…uce eps and add a maximum to numpy.clip().
Faster deconvolution
…tions to optimize on if deterministic results are needed.
…fov and Z value to __init__ and store in 'fov_index' parameter so we have a record of what fov and Z values were used for optimization if 'fov_index' was not specified. Change 'fov_index' to require a both fov and z value for every element.
…z plane filtering
fixing z plane duplicate removal
Add deterministic option for OptimizeIteration
Update license from Zhuang lab
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Hello @LesikDee! Thanks for opening this PR.
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