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1 | | -This is a testing file for the trackmate branch and for the trackmate python class. |
| 1 | +# Testing the `imcflibs.imagej.trackmate` module |
2 | 2 |
|
3 | | -The following Fiji script needs a `.jar` of the trackmate branch to be installed into Fiji already. |
| 3 | +Instructions for *interactive* testing (i.e. manually running a script in Fiji's |
| 4 | +*Script Editor*) of the `imcflibs.imagej.trackmate` module. |
4 | 5 |
|
5 | | -You can open the a blobs image (`CTRL+SHIFT+B`) and then run the following script: |
| 6 | +## Testing instructions |
6 | 7 |
|
7 | | -```python |
| 8 | +1. An updated `python-imcflibs.jar` containing the changes to be tested has to |
| 9 | + be installed into Fiji already. |
| 10 | +1. Next, open the blobs image, e.g. using `Ctrl` + `Shift` + `B`. |
| 11 | +1. Then, launch the *Script Editor* using `Ctrl` + `Shift` + `N`, paste the |
| 12 | + following script and finally run it: |
| 13 | + |
| 14 | +```Python |
8 | 15 | from imcflibs.imagej import trackmate |
9 | 16 | from ij import IJ |
10 | 17 |
|
11 | 18 | imp = IJ.getImage() |
12 | | -# Detector |
| 19 | + |
| 20 | +# Select the trackmate LoG detector: |
13 | 21 | settings = trackmate.log_detector(imp, 5, 1, 0) |
14 | | -# settings = trackmate.cellpose_detector(imp, "S:\cellpose_env", "NUCLEI", 23.0, 1, 0) # WORKS, tested |
15 | | -# settings = trackmate.stardist_detector(imp, 1) # WORKS, tested |
16 | 22 |
|
17 | | -# Manual tracker addition, run_trackmate does this otherwise |
| 23 | +# Alternatively, use the Cellpose or StarDist detector: |
| 24 | +# settings = trackmate.cellpose_detector(imp, "S:\cellpose_env", "NUCLEI", 23.0, 1, 0) |
| 25 | +# settings = trackmate.stardist_detector(imp, 1) |
| 26 | + |
| 27 | +# Manual tracker addition, run_trackmate does this otherwise: |
18 | 28 | # settings = trackmate.sparseLAP_tracker(settings) |
19 | 29 |
|
20 | | -# Spot and track filtering |
| 30 | +# Spot and track filtering: |
21 | 31 | # settings = trackmate.spot_filtering(settings, None, 1.0, None, None) |
22 | 32 | # settings = trackmate.track_filtering(settings, 15.0, 15.0, 3, 1, 1) |
23 | 33 |
|
24 | 34 | res_img = trackmate.run_trackmate(imp, settings) |
25 | 35 | res_img.show() |
| 36 | +``` |
26 | 37 |
|
27 | | -``` |
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