Comments (2)
Hi @hugovaysset - thanks - I hope it's proving useful!
We've been meaning to update the documentation for a while. There's a new CONFIGURATION.md
in the root directory with some details now. Can you let me know which parameters in particular you're having trouble with?
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Hi @quantumjot, thanks for the quick answer!
Actually, my questions are very broad and basic about the algorithm that is used in btrack.
I solved the computation time issue by just removing the optimisation step. What is the point of this step ? In other words, what do I loose when I don't do it ? I suppose that this step can substantially increase the quality of the tracking results, so I would like to better understand it. In issue #13, you said "you probably need to change some parameters in the config to better to describe what you are trying to track and what you care about.". Could you please tell me more about which parameters are the most important ones ? Are they more in the Motion model or in the Hypothesis model? I suppose that the number and the type of hypotheses that we test must be important, should I tune them to save computational time? Is the precise value of each numerical parameter in the Hypothesis model (lambda_time, lambda_dist, eta, etc.) really important?
Additionally, I would also be interested in knowing what could be done with the Object model (that is empty in the config file given in the documentation). Is it possible to describe the cells that we want to track, in order to integrate not only the position but also for example the surface of the cells to improve the quality of the tracking results ?
Thanks again.
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Related Issues (20)
- [FEATURE REQUEST] Update napari hub preview page with new plugin details
- [FEATURE REQUEST] Should example configs be taken from `lowe-lab-ucl/btrack-examples`? HOT 2
- [FEATURE REQUEST] Remove default values for `napari` widgets
- `generation` missing from list of `Tracklet` attributes
- [BUG] Values in `Optimiser` tab aren't being updated from config HOT 3
- [FEATURE REQUEST] Add a warning if `enable_optimisation == False` but optimising HOT 1
- [FEATURE REQUEST] In tests change `prob_not_assign` to `0.001` HOT 1
- [FEATURE REQUEST] If `enable_optimisation` is False then disable tab/nested widgets HOT 2
- [FEATURE REQUEST] Rename `Method` tab to `Basic` HOT 1
- [BUG] `volume` isn't set as expected, in the `test_tracker_graph` test HOT 4
- [FEATURE REQUEST] Write a test for the new `enable_optimisation` flag
- [BUG] Default config name is used when saving config from napari plugin HOT 8
- [BUG] configuration volume is None HOT 2
- [FEATURE REQUEST] 2D tracking with no branching and short links HOT 2
- [FEATURE REQUEST] Vector field to aid tracking HOT 5
- [BUG] not all objects passed to btrack are tracked - some seem to get lost HOT 1
- Filter tracks by value HOT 2
- [FEATURE REQUEST] Add constraints to tracking and possibly variable search radius.
- [FEATURE REQUEST] Better documentation on the config file
- combine cellpose segmentation with tracking result into h5 file[FEATURE REQUEST] HOT 2
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