Import spots from label images #79
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src/test/java/org/mastodon/mamut/io/importer/labelimage/ui/ImportSpotsFromImgPlusViewDemo.java
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* The frameId previously used to update progress could in some cases be higher than numTimepoints.
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…fully run the command and see the results Co-authored-by: Matthias Arzt <[email protected]>
…s math to compute it
…) and importSpotsFromBdvChannel()
…ions in method createSpotsFromLabelImage() by SequenceDescription, which contains them both
* Results are seen with less user interaction (zooming, paning)
…spot conversion can be seen.
That's a good idea. The sigma was too mathematical for the users. I changed it.
They exist now for both import options. Thanks for your input. |
I agree with you. I decided to keep the code simple at the expense for more computations. |
…ve time points having the same label
…portSpotsFromBdvChannelView and ImportSpotsFromImgPlusView commands
* Add unit test covering a splitting event for method linkSpotsWithSameLabel
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This PR adds a plugin to convert label images to (spot) ellipsoids.
This functionality can be handy, if a segmentation of 3D time lapse images had been performed outside Mastodon users want to make use of these segmentation inside a Mastodon project.
Notes from https://github.com/Noam-Dori who contributed to this:
To accomplish the targeted functionality, the plugin runs twice through each image read.
Once to determine maximum/minimum values per frame for array initialization, and once to do summation for covariance & mean. It might be possible to reduce this to 1 run either by finding the min/max stored in the metadata of the image (this is a common and very useful property so it might exist in there), or by changing from an array model to a Hashmap model (at the expense of memory).
It seems mastodon draws the ellipsoid at 1σ, which only includes ~46% of the target ellipsoid. This is not what we are looking for. Therefore I set it to draw the ellipsoid at a default 2.1σ, which when squared yields the 5 in the calculation. Since this is an empirical choice I also included it as a parameter in the plugin dialog.
Replaces #47
Since during the development some memory issue during the test process occurred, this PR adds some optimizations for running unit tests for less memory consumption.
Resolves #83