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klasma / BaxterAlgorithms

Software for segmentation, tracking and analysis of cells in microscope image sequences.
MIT License
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stopped in "segmentation Done" #8

Open wyp2010s opened 5 years ago

wyp2010s commented 5 years ago

BaxterAlgorithms Wrote to the settings file of D:\test Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 1 clusters into 5 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Separating 1 clusters into 4 cells using the watershed transform Separating 1 clusters into 9 cells using the watershed transform Separating 7 clusters into 25 cells using the watershed transform Wrote to the settings file of D:\照片素材 Separating 1 clusters into 1180 cells using the watershed transform Separating 1 clusters into 636 cells using the watershed transform Separating 1 clusters into 636 cells using the watershed transform Separating 1 clusters into 636 cells using the watershed transform Separating 1 clusters into 1180 cells using the watershed transform Wrote to the settings file of D:\照片素材 Separating 101 clusters into 271 cells using the watershed transform Separating 101 clusters into 271 cells using the watershed transform Wrote to file D:\照片素材\Settings.csv Tracking cells in D:\照片素材\aglz- Starting parallel pool (parpool) using the 'local' profile ... connected to 8 workers. Segmenting image 1 / 100 Segmenting image 2 / 100 Segmenting image 3 / 100 Segmenting image 5 / 100 Segmenting image 8 / 100 Segmenting image 12 / 100 Segmenting image 18 / 100 Segmenting image 25 / 100 Separating 91 clusters into 250 cells using the watershed transform Separating 105 clusters into 296 cells using the watershed transform Separating 101 clusters into 271 cells using the watershed transform Computing features for image 1 / 100 Computing features for image 2 / 100 Separating 88 clusters into 278 cells using the watershed transform Computing features for image 3 / 100 Separating 102 clusters into 295 cells using the watershed transform Computing features for image 5 / 100 Separating 87 clusters into 258 cells using the watershed transform Computing features for image 8 / 100 Computing features for image 12 / 100 Separating 100 clusters into 295 cells using the watershed transform Computing features for image 18 / 100 Separating 105 clusters into 283 cells using the watershed transform Computing features for image 25 / 100 Segmenting image 7 / 100 Separating 104 clusters into 286 cells using the watershed transform Segmenting image 11 / 100 Separating 94 clusters into 260 cells using the watershed transform Segmenting image 32 / 100 Separating 102 clusters into 287 cells using the watershed transform Segmenting image 39 / 100 Separating 95 clusters into 288 cells using the watershed transform Segmenting image 46 / 100 Separating 91 clusters into 267 cells using the watershed transform Segmenting image 4 / 100 Separating 98 clusters into 280 cells using the watershed transform Computing features for image 4 / 100 Computing features for image 7 / 100 Computing features for image 11 / 100 Segmenting image 17 / 100 Separating 94 clusters into 279 cells using the watershed transform Computing features for image 17 / 100 Segmenting image 24 / 100 Separating 85 clusters into 267 cells using the watershed transform Computing features for image 24 / 100 Computing features for image 32 / 100 Computing features for image 39 / 100 Segmenting image 38 / 100 Computing features for image 46 / 100 Segmenting image 53 / 100 Segmenting image 23 / 100 Separating 97 clusters into 288 cells using the watershed transform Segmenting image 31 / 100 Separating 94 clusters into 284 cells using the watershed transform Separating 99 clusters into 323 cells using the watershed transform Computing features for image 38 / 100 Segmenting image 45 / 100 Separating 94 clusters into 275 cells using the watershed transform Computing features for image 45 / 100 Segmenting image 6 / 100 Separating 97 clusters into 293 cells using the watershed transform Computing features for image 6 / 100 Segmenting image 10 / 100 Separating 98 clusters into 280 cells using the watershed transform Computing features for image 10 / 100 Segmenting image 16 / 100 Separating 90 clusters into 263 cells using the watershed transform Computing features for image 16 / 100 Computing features for image 23 / 100 Computing features for image 31 / 100 Separating 97 clusters into 273 cells using the watershed transform Computing features for image 53 / 100 Segmenting image 59 / 100 Segmenting image 30 / 100 Separating 96 clusters into 290 cells using the watershed transform Computing features for image 30 / 100 Segmenting image 37 / 100 Separating 94 clusters into 286 cells using the watershed transform Computing features for image 37 / 100 Segmenting image 44 / 100 Separating 97 clusters into 293 cells using the watershed transform Computing features for image 44 / 100 Segmenting image 52 / 100 Separating 91 clusters into 283 cells using the watershed transform Computing features for image 52 / 100 Segmenting image 9 / 100 Separating 91 clusters into 253 cells using the watershed transform Computing features for image 9 / 100 Segmenting image 15 / 100 Separating 104 clusters into 291 cells using the watershed transform Computing features for image 15 / 100 Segmenting image 22 / 100 Separating 95 clusters into 264 cells using the watershed transform Computing features for image 22 / 100 Segmenting image 29 / 100 Separating 96 clusters into 296 cells using the watershed transform Segmenting image 36 / 100 Separating 87 clusters into 276 cells using the watershed transform Segmenting image 43 / 100 Separating 99 clusters into 286 cells using the watershed transform Segmenting image 51 / 100 Separating 89 clusters into 275 cells using the watershed transform Separating 104 clusters into 294 cells using the watershed transform Computing features for image 59 / 100 Segmenting image 65 / 100 Segmenting image 21 / 100 Separating 89 clusters into 250 cells using the watershed transform Computing features for image 29 / 100 Computing features for image 36 / 100 Computing features for image 43 / 100 Computing features for image 51 / 100 Segmenting image 58 / 100 Separating 113 clusters into 312 cells using the watershed transform Computing features for image 58 / 100 Separating 101 clusters into 298 cells using the watershed transform Computing features for image 65 / 100 Segmenting image 14 / 100 Separating 108 clusters into 304 cells using the watershed transform Computing features for image 14 / 100 Computing features for image 21 / 100 Segmenting image 57 / 100 Separating 106 clusters into 304 cells using the watershed transform Segmenting image 13 / 100 Separating 90 clusters into 247 cells using the watershed transform Computing features for image 13 / 100 Segmenting image 20 / 100 Separating 100 clusters into 286 cells using the watershed transform Computing features for image 20 / 100 Segmenting image 28 / 100 Separating 98 clusters into 291 cells using the watershed transform Computing features for image 28 / 100 Segmenting image 35 / 100 Separating 97 clusters into 297 cells using the watershed transform Computing features for image 35 / 100 Segmenting image 42 / 100 Separating 93 clusters into 276 cells using the watershed transform Computing features for image 42 / 100 Segmenting image 50 / 100 Separating 92 clusters into 276 cells using the watershed transform Computing features for image 50 / 100 Computing features for image 57 / 100 Segmenting image 64 / 100 Separating 100 clusters into 304 cells using the watershed transform Computing features for image 64 / 100 Segmenting image 19 / 100 Separating 94 clusters into 266 cells using the watershed transform Computing features for image 19 / 100 Segmenting image 27 / 100 Separating 96 clusters into 290 cells using the watershed transform Computing features for image 27 / 100 Segmenting image 34 / 100 Separating 96 clusters into 299 cells using the watershed transform Computing features for image 34 / 100 Segmenting image 41 / 100 Separating 93 clusters into 272 cells using the watershed transform Computing features for image 41 / 100 Segmenting image 40 / 100 Separating 90 clusters into 272 cells using the watershed transform Segmenting image 49 / 100 Separating 91 clusters into 271 cells using the watershed transform Computing features for image 49 / 100 Segmenting image 56 / 100 Separating 104 clusters into 297 cells using the watershed transform Computing features for image 56 / 100 Segmenting image 63 / 100 Separating 112 clusters into 320 cells using the watershed transform Computing features for image 63 / 100 Segmenting image 70 / 100 Separating 96 clusters into 300 cells using the watershed transform Computing features for image 70 / 100 Segmenting image 26 / 100 Separating 102 clusters into 286 cells using the watershed transform Computing features for image 26 / 100 Segmenting image 33 / 100 Separating 84 clusters into 260 cells using the watershed transform Computing features for image 33 / 100 Computing features for image 40 / 100 Segmenting image 48 / 100 Separating 95 clusters into 262 cells using the watershed transform Computing features for image 48 / 100 Segmenting image 74 / 100 Segmenting image 78 / 100 Segmenting image 47 / 100 Separating 100 clusters into 290 cells using the watershed transform Computing features for image 47 / 100 Segmenting image 55 / 100 Separating 98 clusters into 287 cells using the watershed transform Computing features for image 55 / 100 Segmenting image 62 / 100 Separating 91 clusters into 267 cells using the watershed transform Computing features for image 62 / 100 Segmenting image 69 / 100 Separating 101 clusters into 306 cells using the watershed transform Computing features for image 69 / 100 Separating 105 clusters into 286 cells using the watershed transform Computing features for image 74 / 100 Segmenting image 84 / 100 Segmenting image 81 / 100 Segmenting image 54 / 100 Separating 88 clusters into 261 cells using the watershed transform Computing features for image 54 / 100 Segmenting image 61 / 100 Separating 107 clusters into 302 cells using the watershed transform Computing features for image 61 / 100 Segmenting image 60 / 100 Separating 107 clusters into 296 cells using the watershed transform Segmenting image 68 / 100 Separating 95 clusters into 302 cells using the watershed transform Computing features for image 68 / 100 Segmenting image 73 / 100 Separating 111 clusters into 316 cells using the watershed transform Separating 94 clusters into 263 cells using the watershed transform Computing features for image 84 / 100 Separating 100 clusters into 301 cells using the watershed transform Computing features for image 78 / 100 Segmenting image 77 / 100 Separating 103 clusters into 310 cells using the watershed transform Separating 102 clusters into 296 cells using the watershed transform Computing features for image 81 / 100 Segmenting image 86 / 100 Segmenting image 88 / 100 Computing features for image 60 / 100 Computing features for image 73 / 100 Segmenting image 83 / 100 Separating 97 clusters into 301 cells using the watershed transform Computing features for image 77 / 100 Segmenting image 80 / 100 Separating 107 clusters into 285 cells using the watershed transform Segmenting image 67 / 100 Separating 100 clusters into 285 cells using the watershed transform Computing features for image 67 / 100 Segmenting image 72 / 100 Separating 99 clusters into 312 cells using the watershed transform Computing features for image 72 / 100 Computing features for image 83 / 100 Segmenting image 82 / 100 Segmenting image 76 / 100 Separating 106 clusters into 318 cells using the watershed transform Computing features for image 80 / 100 Segmenting image 79 / 100 Separating 109 clusters into 318 cells using the watershed transform Separating 110 clusters into 311 cells using the watershed transform Computing features for image 86 / 100 Segmenting image 85 / 100 Separating 98 clusters into 293 cells using the watershed transform Separating 111 clusters into 298 cells using the watershed transform Computing features for image 88 / 100 Segmenting image 90 / 100 Segmenting image 66 / 100 Separating 95 clusters into 275 cells using the watershed transform Computing features for image 66 / 100 Separating 106 clusters into 318 cells using the watershed transform Computing features for image 82 / 100 Computing features for image 76 / 100 Computing features for image 79 / 100 Computing features for image 85 / 100 Segmenting image 87 / 100 Separating 104 clusters into 282 cells using the watershed transform Computing features for image 87 / 100 Separating 106 clusters into 296 cells using the watershed transform Computing features for image 90 / 100 Segmenting image 71 / 100 Separating 99 clusters into 288 cells using the watershed transform Computing features for image 71 / 100 Segmenting image 97 / 100 Segmenting image 95 / 100 Segmenting image 96 / 100 Segmenting image 98 / 100 Segmenting image 89 / 100 Separating 100 clusters into 287 cells using the watershed transform Computing features for image 89 / 100 Segmenting image 92 / 100 Segmenting image 93 / 100 Segmenting image 75 / 100 Separating 93 clusters into 284 cells using the watershed transform Computing features for image 75 / 100 Separating 94 clusters into 271 cells using the watershed transform Computing features for image 97 / 100 Separating 100 clusters into 292 cells using the watershed transform Computing features for image 98 / 100 Segmenting image 99 / 100 Separating 97 clusters into 284 cells using the watershed transform Computing features for image 92 / 100 Separating 100 clusters into 294 cells using the watershed transform Computing features for image 95 / 100 Segmenting image 94 / 100 Separating 115 clusters into 316 cells using the watershed transform Computing features for image 96 / 100 Separating 93 clusters into 267 cells using the watershed transform Computing features for image 93 / 100 Segmenting image 100 / 100 Separating 98 clusters into 299 cells using the watershed transform Separating 110 clusters into 300 cells using the watershed transform Computing features for image 99 / 100 Segmenting image 91 / 100 Separating 112 clusters into 306 cells using the watershed transform Computing features for image 91 / 100 Separating 108 clusters into 313 cells using the watershed transform Computing features for image 94 / 100 Computing features for image 100 / 100 Segmentation Done.

AFTER segmentation ,it seems that program is end , but i saw there's a tracking process in next.

klasma commented 5 years ago

My guess is that the software is busy computing migration probabilities and mitosis probabilities. This can take a long time (several hours) if you have a lot (thousands) of segmented objects in each frame. Unfortunately, there are no prinouts in the methods which compute probabilites. That is something I will add in the future. Try leaving the software overnight to see if it gets to the track linking. If that does not work, you can try pressing the pause button in Matlab to see what the program is doing.

The following information would be useful:

What operating system do you have? Are you running the program in Matlab or are you running the standalone version? For how long did you wait? How many objects do you have in each frame?

klasma commented 5 years ago

You should also take a look at how much RAM the program is using. The run time will be shorter and you will need less RAM i you do not allow cell division, by setting pSplit to 0 in the tracking settings. You can try that if waiting is not enough.