Restructure biahub #61
Conversation
ieivanov
requested review from
talonchandler,
edyoshikun,
tayllatheodoro and
ziw-liu
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@tayllatheodoro (cc: @ieivanov), please run an integration test with https://github.com/czbiohub-sf/mantis-analysis-template. Please report here if any of the steps don't work as expected. |
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| from pystackreg import StackReg | |||
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Instead of using StackReg, I suggest implementing or reusing the 3D phase cross correlation that @edyoshikun may have implemented as part of autotracker algorithm. 3D phase cross correlation should work well with bead images. Perhaps you tried and decided that you need to handle XY and Z-registration separately.
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Is ants useful here?
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@ieivanov having methods and the CLI in the same file does make code quite readable. Most methods have docstrings, but a few do not.
The logic and algorithms for registration and stabilization steps require an iteration. Let's brainstorm tomorrow or Thursday.
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Just ran a very basic deconvolution integration test on this branch, and all worked as expected.
My only minor suggestion is to consider renaming AnalysisSettings.py to analysis_settings.py or just settings.py. Right now AnalysisSettings.py sticks out as the only CamelCase file.
Restructure repo as discussed in #52