Code

Import spots from label images#79

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stefanhahmann merged 38 commits intomastermastodon-sc/mastodon-deep-lineage:masterfrom import_spotsmastodon-sc/mastodon-deep-lineage:import_spotsCopy head branch name to clipboardMar 20, 2024

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Commits on Mar 11, 2024

• Add commons-math with scope test to pom.xml

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• Add class Covariance that can compute Covariance matrices using an online algorithm

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• Add class CovarianceMatrix that can compute Covariance matrices using an online algorithm

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• Add class Mean and MeansVector that can compute mean(s) using an online algorithm

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• Add demo show mean and covariance computation using two-pass and online algorithms

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• Add a new utility class that contains methods to create Spots from Label images

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• Add new Scijava command to start importing spots from a Fiji Image (aka ImgPlus image)

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• Add new Scijava command to start importing spots from a user selected BDV channel

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• Add new Plugin ImportSpotsFromLabelImagePlugin

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• Add new test class MeansVectorTest

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• Remove IllegalArgumentException regarding a condition that should not occur

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• Set active maven profile via settings file

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• Change settings so that sonar and build job can use 1g ram

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• Do not create a new context in DemoUtils but reuse an existing one that will be closed outside

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• Set sigma to default to 2.1 as this seems to yield the best results

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• Remove creating new Context() from ExportLabelImageControllerTest

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Commits on Mar 15, 2024

• Replace channel index selection for BDV channel import by BDV source selection

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• Change menu entry to "Import spots from label image"

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• Make showing progress in the status service more correct.

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• An improved version of ImportSpotsFromImgPlusViewDemo that allows to fully run the command and see the results

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• Hard code results for Covariance tests instead of using apache commons math to compute it

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• Streamline the order of params in the methods importSpotsFromImgPlus() and importSpotsFromBdvChannel()

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• Reduce code redundancy by replacing the params frames and voxelDimensions in method createSpotsFromLabelImage() by SequenceDescription, which contains them both

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• Fix dimensions settings in ImportSpotsFromImgPlusViewDemo

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• Move generation of example image from ImportSpotsFromImgPlusViewDemo to DemoUtils

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• Change ImportSpotsFromBdvChannelViewDemo so that the actual image to spot conversion can be seen.

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• Change user input from sigma to ellipsoid scaling factor

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• Reuse means computed in CovarianceMatrix instead of re-computing them in Means class

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• Extract method getSourceNames() to separate method and provide unit test

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Commits on Mar 19, 2024

• Add method to LineageTreeUtils that allows linking spots in consecutive time points having the same label

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• Refactored sub-package demo to util in test/../io/importer/labelimage

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• Change some debug messages to cover potential plurals of variables

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• Remove obsolete imports in test and demo classes

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• Add option to link spots with same labels in consecutive frames to ImportSpotsFromBdvChannelView and ImportSpotsFromImgPlusView commands

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• Add splitting case to method description of linkSpotsWithSameLabel()

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• Add documentation for importing spots from labels to README.md

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• Add Imports to table of contents of README.md

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• Add info regarding linking to import spots from labels section in README.md

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