Revision 27fa41066bf09a3c1ca00fd333f72755e481b16f authored by H.F on 13 April 2021, 10:57:05 UTC, committed by H.F on 13 April 2021, 10:57:05 UTC
1 parent f3455fe
test14.log.1
Processing /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200314, output /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200314_result/output
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T07:18:45.567 Loading 21
222.457783 seconds (3.42 M allocations: 34.673 GiB, 0.39% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
126.070841 seconds (348.19 M allocations: 75.176 GiB, 36.41% gc time)
Finding connected component
7.208236 seconds (179.85 k allocations: 4.936 GiB, 0.15% gc time)
Detecting contacted branch
6.246888 seconds (1.37 M allocations: 54.239 GiB, 19.28% gc time)
Found contacted branch: [1, 3, 6, 10]
Splitting branch 1 now
Finding connected component
Reassigning contacted branch 1
Branch 1 -> 100
Splitting branch 3 now
Finding connected component
Reassigning contacted branch 3
Branch 3 -> 101
Branch 3 -> 102
Splitting branch 6 now
Finding connected component
Reassigning contacted branch 6
Branch 6 -> 103
Splitting branch 10 now
Finding connected component
Reassigning contacted branch 10
Branch 10 -> 104
48.620855 seconds (4.37 M allocations: 121.852 GiB, 9.21% gc time)
Grant domain for each detected cell by watershed
51.644902 seconds (1.81 M allocations: 27.987 GiB, 42.54% gc time)
Drawing longlived_maps
[7, 9, 13, 16, 19, 23, 29, 100, 101, 102, 103, 104]
58.253263 seconds (1.90 M allocations: 32.597 GiB, 38.61% gc time)
tracking cell 1
6.284875 seconds (20.95 M allocations: 3.690 GiB, 58.08% gc time)
Extracting nucleus
14.877992 seconds (8.86 M allocations: 27.142 GiB, 49.49% gc time)
2.051621 seconds (2.75 M allocations: 3.927 GiB, 2.79% gc time)
tracking cell 2
3.643177 seconds (20.01 M allocations: 3.611 GiB, 38.62% gc time)
Extracting nucleus
11.962821 seconds (1.98 M allocations: 26.844 GiB, 59.05% gc time)
1.246336 seconds (3.10 k allocations: 3.834 GiB, 1.96% gc time)
tracking cell 3
2.248838 seconds (11.51 M allocations: 2.597 GiB, 24.59% gc time)
Extracting nucleus
12.971558 seconds (1.98 M allocations: 26.559 GiB, 63.79% gc time)
1.219404 seconds (3.10 k allocations: 3.834 GiB, 1.11% gc time)
tracking cell 4
2.390074 seconds (11.69 M allocations: 2.619 GiB, 22.44% gc time)
Extracting nucleus
15.845084 seconds (1.97 M allocations: 26.478 GiB, 72.76% gc time)
1.173056 seconds (3.07 k allocations: 3.793 GiB, 1.45% gc time)
tracking cell 5
2.753382 seconds (13.49 M allocations: 2.833 GiB, 36.02% gc time)
Extracting nucleus
11.920499 seconds (1.97 M allocations: 26.624 GiB, 63.75% gc time)
1.168830 seconds (3.09 k allocations: 3.798 GiB, 1.00% gc time)
tracking cell 6
1.642772 seconds (8.44 M allocations: 2.232 GiB, 0.18% gc time)
Extracting nucleus
12.962116 seconds (1.97 M allocations: 26.424 GiB, 64.43% gc time)
1.199575 seconds (3.07 k allocations: 3.794 GiB, 1.26% gc time)
tracking cell 7
2.644350 seconds (13.90 M allocations: 2.882 GiB, 28.49% gc time)
Extracting nucleus
14.944183 seconds (1.97 M allocations: 26.473 GiB, 70.90% gc time)
1.190640 seconds (3.07 k allocations: 3.803 GiB, 1.12% gc time)
tracking cell 8
4.556056 seconds (22.89 M allocations: 3.954 GiB, 36.52% gc time)
Extracting nucleus
12.094564 seconds (1.98 M allocations: 26.818 GiB, 60.96% gc time)
1.156030 seconds (3.07 k allocations: 3.815 GiB, 1.27% gc time)
tracking cell 9
3.593645 seconds (18.78 M allocations: 3.464 GiB, 36.49% gc time)
Extracting nucleus
12.317823 seconds (1.98 M allocations: 26.804 GiB, 62.54% gc time)
1.174582 seconds (3.10 k allocations: 3.820 GiB, 1.18% gc time)
tracking cell 10
2.822396 seconds (13.60 M allocations: 2.846 GiB, 35.89% gc time)
Extracting nucleus
11.588283 seconds (1.98 M allocations: 26.744 GiB, 62.73% gc time)
1.168522 seconds (3.10 k allocations: 3.798 GiB, 1.26% gc time)
tracking cell 11
3.565569 seconds (15.89 M allocations: 3.119 GiB, 32.46% gc time)
Extracting nucleus
14.054183 seconds (1.97 M allocations: 26.633 GiB, 70.93% gc time)
1.171729 seconds (3.07 k allocations: 3.803 GiB, 1.24% gc time)
tracking cell 12
4.345496 seconds (23.03 M allocations: 3.971 GiB, 36.76% gc time)
Extracting nucleus
11.662723 seconds (1.98 M allocations: 26.870 GiB, 60.06% gc time)
1.203524 seconds (3.10 k allocations: 3.841 GiB, 1.35% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T07:34:04.039 Loading 22
221.408802 seconds (2.02 M allocations: 34.597 GiB, 0.18% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
89.596337 seconds (332.12 M allocations: 74.401 GiB, 44.80% gc time)
Finding connected component
5.645244 seconds (523 allocations: 4.925 GiB, 0.17% gc time)
Detecting contacted branch
4.210997 seconds (72.82 k allocations: 29.555 GiB, 30.77% gc time)
Found contacted branch: [1, 33, 37]
Splitting branch 1 now
Finding connected component
Reassigning contacted branch 1
Branch 1 -> 100
Splitting branch 33 now
Finding connected component
Reassigning contacted branch 33
Splitting branch 37 now
Finding connected component
Reassigning contacted branch 37
26.441602 seconds (85.38 k allocations: 80.176 GiB, 11.21% gc time)
Grant domain for each detected cell by watershed
45.942470 seconds (18.93 k allocations: 29.249 GiB, 27.11% gc time)
Drawing longlived_maps
[7, 11, 33, 34, 37, 100]
51.008904 seconds (19.17 k allocations: 33.854 GiB, 25.37% gc time)
tracking cell 1
7.076488 seconds (26.47 M allocations: 4.380 GiB, 61.88% gc time)
Extracting nucleus
10.169187 seconds (1.98 M allocations: 26.888 GiB, 58.27% gc time)
0.669052 seconds (3.10 k allocations: 3.795 GiB, 2.01% gc time)
tracking cell 2
2.253876 seconds (13.96 M allocations: 2.890 GiB, 37.69% gc time)
Extracting nucleus
13.527809 seconds (1.98 M allocations: 26.712 GiB, 70.87% gc time)
0.694063 seconds (3.10 k allocations: 3.799 GiB, 2.08% gc time)
tracking cell 3
2.670396 seconds (15.11 M allocations: 3.027 GiB, 33.03% gc time)
Extracting nucleus
13.920745 seconds (1.97 M allocations: 26.511 GiB, 72.63% gc time)
0.750898 seconds (3.07 k allocations: 3.806 GiB, 1.67% gc time)
tracking cell 4
2.432735 seconds (11.04 M allocations: 2.541 GiB, 23.98% gc time)
Extracting nucleus
15.644595 seconds (1.97 M allocations: 26.477 GiB, 73.19% gc time)
0.680089 seconds (3.07 k allocations: 3.795 GiB, 1.89% gc time)
tracking cell 5
3.639636 seconds (16.34 M allocations: 3.173 GiB, 33.63% gc time)
Extracting nucleus
13.573005 seconds (1.97 M allocations: 26.538 GiB, 69.47% gc time)
0.848596 seconds (3.07 k allocations: 3.841 GiB, 1.51% gc time)
tracking cell 6
3.341064 seconds (15.96 M allocations: 3.127 GiB, 25.39% gc time)
Extracting nucleus
16.505143 seconds (1.98 M allocations: 26.673 GiB, 69.01% gc time)
0.773372 seconds (3.10 k allocations: 3.836 GiB, 1.90% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T07:44:24.325 Loading 23
220.683071 seconds (24.07 k allocations: 34.506 GiB, 0.16% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
103.653985 seconds (332.25 M allocations: 74.403 GiB, 41.62% gc time)
Finding connected component
5.944324 seconds (475 allocations: 4.926 GiB, 0.18% gc time)
Detecting contacted branch
5.161766 seconds (105.31 k allocations: 49.257 GiB, 21.50% gc time)
Found contacted branch: [5, 10, 11]
Splitting branch 5 now
Finding connected component
Reassigning contacted branch 5
Branch 5 -> 100
Splitting branch 10 now
Finding connected component
Reassigning contacted branch 10
Splitting branch 11 now
Finding connected component
Reassigning contacted branch 11
Branch 11 -> 101
30.185881 seconds (130.45 k allocations: 99.878 GiB, 9.93% gc time)
Grant domain for each detected cell by watershed
43.679346 seconds (19.63 k allocations: 27.855 GiB, 30.08% gc time)
Drawing longlived_maps
[1, 3, 4, 7, 10, 12, 27, 28, 100, 101]
49.269586 seconds (19.89 k allocations: 32.460 GiB, 27.68% gc time)
tracking cell 1
3.020640 seconds (14.20 M allocations: 2.918 GiB, 41.76% gc time)
Extracting nucleus
14.614171 seconds (1.97 M allocations: 26.651 GiB, 69.49% gc time)
0.867932 seconds (3.09 k allocations: 3.797 GiB, 1.57% gc time)
tracking cell 2
2.570765 seconds (14.13 M allocations: 2.910 GiB, 27.42% gc time)
Extracting nucleus
11.847237 seconds (1.98 M allocations: 26.759 GiB, 63.40% gc time)
0.888701 seconds (3.10 k allocations: 3.793 GiB, 1.50% gc time)
tracking cell 3
3.243551 seconds (19.96 M allocations: 3.605 GiB, 46.07% gc time)
Extracting nucleus
10.520352 seconds (1.98 M allocations: 26.835 GiB, 58.91% gc time)
0.657834 seconds (3.10 k allocations: 3.786 GiB, 2.13% gc time)
tracking cell 4
4.089308 seconds (22.88 M allocations: 3.953 GiB, 45.47% gc time)
Extracting nucleus
12.201517 seconds (1.98 M allocations: 26.871 GiB, 63.40% gc time)
0.637321 seconds (3.10 k allocations: 3.808 GiB, 2.11% gc time)
tracking cell 5
3.218593 seconds (20.01 M allocations: 3.611 GiB, 48.30% gc time)
Extracting nucleus
14.942738 seconds (1.98 M allocations: 26.733 GiB, 70.00% gc time)
0.864291 seconds (3.10 k allocations: 3.827 GiB, 1.59% gc time)
tracking cell 6
3.549317 seconds (17.87 M allocations: 3.356 GiB, 36.74% gc time)
Extracting nucleus
12.171096 seconds (1.98 M allocations: 26.718 GiB, 67.05% gc time)
0.678523 seconds (3.10 k allocations: 3.822 GiB, 1.93% gc time)
tracking cell 7
0.738102 seconds (4.76 M allocations: 1.793 GiB, 0.42% gc time)
Extracting nucleus
14.106513 seconds (1.97 M allocations: 26.282 GiB, 73.80% gc time)
0.843563 seconds (3.07 k allocations: 3.793 GiB, 1.52% gc time)
tracking cell 8
1.792197 seconds (11.04 M allocations: 2.541 GiB, 28.84% gc time)
Extracting nucleus
13.434980 seconds (1.97 M allocations: 26.551 GiB, 72.08% gc time)
0.640581 seconds (3.07 k allocations: 3.782 GiB, 1.98% gc time)
tracking cell 9
4.719116 seconds (20.50 M allocations: 3.669 GiB, 30.25% gc time)
Extracting nucleus
11.239328 seconds (1.98 M allocations: 26.771 GiB, 63.05% gc time)
0.873787 seconds (3.10 k allocations: 3.791 GiB, 1.59% gc time)
tracking cell 10
5.561436 seconds (27.15 M allocations: 4.462 GiB, 48.04% gc time)
Extracting nucleus
10.865802 seconds (1.98 M allocations: 26.897 GiB, 60.72% gc time)
0.667061 seconds (3.10 k allocations: 3.822 GiB, 2.15% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T07:57:08.522 Loading 24
214.688871 seconds (24.07 k allocations: 34.506 GiB, 0.16% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
116.577461 seconds (332.39 M allocations: 74.405 GiB, 41.34% gc time)
Finding connected component
5.146804 seconds (471 allocations: 4.926 GiB, 0.25% gc time)
Detecting contacted branch
4.112329 seconds (81.58 k allocations: 34.481 GiB, 22.14% gc time)
Found contacted branch: [12, 13, 15, 24]
Splitting branch 12 now
Finding connected component
Reassigning contacted branch 12
Splitting branch 13 now
Finding connected component
Reassigning contacted branch 13
Branch 13 -> 100
Splitting branch 15 now
Finding connected component
Reassigning contacted branch 15
Branch 15 -> 101
Splitting branch 24 now
Finding connected component
Reassigning contacted branch 24
40.443813 seconds (106.97 k allocations: 101.976 GiB, 10.50% gc time)
Grant domain for each detected cell by watershed
39.805960 seconds (19.31 k allocations: 28.451 GiB, 32.42% gc time)
Drawing longlived_maps
[5, 6, 7, 12, 24, 100, 101]
46.330233 seconds (19.55 k allocations: 33.056 GiB, 28.96% gc time)
tracking cell 1
5.765006 seconds (22.22 M allocations: 3.874 GiB, 53.11% gc time)
Extracting nucleus
10.531251 seconds (1.98 M allocations: 26.821 GiB, 61.25% gc time)
0.837441 seconds (3.09 k allocations: 3.787 GiB, 1.59% gc time)
tracking cell 2
4.174960 seconds (22.91 M allocations: 3.956 GiB, 42.55% gc time)
Extracting nucleus
11.933232 seconds (1.98 M allocations: 26.846 GiB, 64.21% gc time)
0.829127 seconds (3.10 k allocations: 3.799 GiB, 1.53% gc time)
tracking cell 3
5.039693 seconds (25.64 M allocations: 4.282 GiB, 43.92% gc time)
Extracting nucleus
10.632943 seconds (1.98 M allocations: 26.881 GiB, 60.93% gc time)
0.648150 seconds (3.10 k allocations: 3.824 GiB, 2.27% gc time)
tracking cell 4
3.878092 seconds (19.91 M allocations: 3.599 GiB, 48.79% gc time)
Extracting nucleus
10.904909 seconds (1.98 M allocations: 26.807 GiB, 58.46% gc time)
0.694358 seconds (3.09 k allocations: 3.813 GiB, 1.91% gc time)
tracking cell 5
1.864243 seconds (12.94 M allocations: 2.768 GiB, 28.51% gc time)
Extracting nucleus
14.863562 seconds (1.97 M allocations: 26.559 GiB, 73.59% gc time)
0.638470 seconds (3.07 k allocations: 3.788 GiB, 2.05% gc time)
tracking cell 6
2.668715 seconds (16.86 M allocations: 3.235 GiB, 34.24% gc time)
Extracting nucleus
18.339762 seconds (1.97 M allocations: 26.628 GiB, 76.95% gc time)
0.841293 seconds (3.08 k allocations: 3.813 GiB, 1.63% gc time)
tracking cell 7
2.567760 seconds (17.74 M allocations: 3.341 GiB, 47.86% gc time)
Extracting nucleus
13.733207 seconds (1.98 M allocations: 26.722 GiB, 65.96% gc time)
0.655186 seconds (3.02 k allocations: 3.754 GiB, 2.05% gc time)
real 50m14.324s
user 694m4.496s
sys 45m56.024s
Processing /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200314, output /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200314_result/output
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T08:09:00.021 Loading 25
221.849514 seconds (3.42 M allocations: 34.673 GiB, 0.37% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
113.196064 seconds (348.16 M allocations: 75.176 GiB, 37.03% gc time)
Finding connected component
6.822331 seconds (179.94 k allocations: 4.934 GiB, 0.26% gc time)
Detecting contacted branch
5.945971 seconds (1.43 M allocations: 39.466 GiB, 19.00% gc time)
Found contacted branch: [6, 10, 11, 17, 21]
Splitting branch 6 now
Finding connected component
Reassigning contacted branch 6
Branch 6 -> 100
Splitting branch 10 now
Finding connected component
Reassigning contacted branch 10
Splitting branch 11 now
Finding connected component
Reassigning contacted branch 11
Branch 11 -> 101
Splitting branch 17 now
Finding connected component
Reassigning contacted branch 17
Splitting branch 21 now
Finding connected component
Reassigning contacted branch 21
Branch 21 -> 102
60.021584 seconds (4.07 M allocations: 123.945 GiB, 10.75% gc time)
Grant domain for each detected cell by watershed
49.478518 seconds (1.81 M allocations: 29.392 GiB, 29.55% gc time)
Drawing longlived_maps
[8, 10, 14, 17, 20, 100, 101, 102]
56.185644 seconds (1.90 M allocations: 34.001 GiB, 26.94% gc time)
tracking cell 1
5.809601 seconds (20.45 M allocations: 3.631 GiB, 47.08% gc time)
Extracting nucleus
15.095984 seconds (8.86 M allocations: 27.135 GiB, 49.43% gc time)
2.187676 seconds (2.75 M allocations: 3.907 GiB, 3.05% gc time)
tracking cell 2
4.248601 seconds (19.18 M allocations: 3.512 GiB, 32.99% gc time)
Extracting nucleus
13.335373 seconds (1.98 M allocations: 26.840 GiB, 62.93% gc time)
1.197562 seconds (3.09 k allocations: 3.794 GiB, 2.70% gc time)
tracking cell 3
4.320494 seconds (21.46 M allocations: 3.783 GiB, 37.46% gc time)
Extracting nucleus
13.720850 seconds (1.98 M allocations: 26.865 GiB, 65.73% gc time)
1.206144 seconds (3.10 k allocations: 3.799 GiB, 1.47% gc time)
tracking cell 4
1.829894 seconds (10.23 M allocations: 2.445 GiB, 26.13% gc time)
Extracting nucleus
13.677861 seconds (1.97 M allocations: 26.436 GiB, 68.40% gc time)
1.293761 seconds (3.08 k allocations: 3.940 GiB, 1.61% gc time)
tracking cell 5
2.657260 seconds (11.23 M allocations: 2.564 GiB, 26.55% gc time)
Extracting nucleus
13.178175 seconds (1.98 M allocations: 26.551 GiB, 67.54% gc time)
1.244130 seconds (3.10 k allocations: 3.815 GiB, 1.46% gc time)
tracking cell 6
2.679920 seconds (11.68 M allocations: 2.618 GiB, 22.41% gc time)
Extracting nucleus
12.663408 seconds (1.98 M allocations: 26.545 GiB, 66.89% gc time)
1.286463 seconds (3.10 k allocations: 3.838 GiB, 1.56% gc time)
tracking cell 7
7.366209 seconds (28.86 M allocations: 4.665 GiB, 43.08% gc time)
Extracting nucleus
12.454961 seconds (1.98 M allocations: 26.916 GiB, 61.06% gc time)
1.237325 seconds (3.10 k allocations: 3.828 GiB, 1.43% gc time)
tracking cell 8
2.009149 seconds (8.78 M allocations: 2.272 GiB, 17.93% gc time)
Extracting nucleus
12.876877 seconds (1.97 M allocations: 26.457 GiB, 66.63% gc time)
1.215933 seconds (3.10 k allocations: 3.815 GiB, 1.29% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T08:21:58.511 Loading 26
221.873508 seconds (2.02 M allocations: 34.597 GiB, 0.16% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
119.772634 seconds (332.38 M allocations: 74.405 GiB, 39.51% gc time)
Finding connected component
5.230513 seconds (645 allocations: 4.925 GiB, 0.19% gc time)
Detecting contacted branch
4.229294 seconds (80.38 k allocations: 34.481 GiB, 22.94% gc time)
Found contacted branch: [6, 9]
Splitting branch 6 now
Finding connected component
Reassigning contacted branch 6
Branch 6 -> 100
Splitting branch 9 now
Finding connected component
Reassigning contacted branch 9
21.552128 seconds (105.22 k allocations: 68.228 GiB, 10.40% gc time)
Grant domain for each detected cell by watershed
45.520359 seconds (19.20 k allocations: 28.474 GiB, 26.33% gc time)
Drawing longlived_maps
[1, 2, 9, 10, 26, 33, 100]
51.570588 seconds (19.45 k allocations: 33.080 GiB, 24.18% gc time)
tracking cell 1
4.904641 seconds (19.56 M allocations: 3.557 GiB, 66.70% gc time)
Extracting nucleus
8.683010 seconds (1.98 M allocations: 26.745 GiB, 52.80% gc time)
0.830485 seconds (3.10 k allocations: 3.798 GiB, 1.58% gc time)
tracking cell 2
2.630888 seconds (14.69 M allocations: 2.976 GiB, 40.84% gc time)
Extracting nucleus
12.691941 seconds (1.97 M allocations: 26.569 GiB, 67.10% gc time)
0.755742 seconds (3.08 k allocations: 3.833 GiB, 2.78% gc time)
tracking cell 3
1.804987 seconds (13.16 M allocations: 2.794 GiB, 37.11% gc time)
Extracting nucleus
13.604679 seconds (1.97 M allocations: 26.504 GiB, 67.43% gc time)
0.723570 seconds (3.07 k allocations: 3.821 GiB, 2.36% gc time)
tracking cell 4
4.055777 seconds (21.55 M allocations: 3.794 GiB, 41.73% gc time)
Extracting nucleus
11.015679 seconds (1.98 M allocations: 26.870 GiB, 60.96% gc time)
0.854676 seconds (3.10 k allocations: 3.794 GiB, 1.79% gc time)
tracking cell 5
1.394686 seconds (6.47 M allocations: 1.997 GiB, 21.87% gc time)
Extracting nucleus
13.273165 seconds (1.97 M allocations: 26.327 GiB, 72.04% gc time)
0.691438 seconds (3.07 k allocations: 3.852 GiB, 2.51% gc time)
tracking cell 6
2.711595 seconds (16.15 M allocations: 3.150 GiB, 36.75% gc time)
Extracting nucleus
11.476354 seconds (1.97 M allocations: 26.582 GiB, 66.72% gc time)
0.708606 seconds (3.07 k allocations: 3.779 GiB, 1.89% gc time)
tracking cell 7
5.091950 seconds (25.10 M allocations: 4.217 GiB, 37.22% gc time)
Extracting nucleus
9.431011 seconds (1.98 M allocations: 26.854 GiB, 52.91% gc time)
0.678507 seconds (3.09 k allocations: 3.834 GiB, 1.98% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T08:33:03.032 Loading 27
224.813300 seconds (24.07 k allocations: 34.506 GiB, 0.15% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
116.281362 seconds (332.30 M allocations: 74.404 GiB, 40.94% gc time)
Finding connected component
5.036868 seconds (631 allocations: 4.926 GiB, 0.22% gc time)
Detecting contacted branch
3.803712 seconds (81.22 k allocations: 34.481 GiB, 21.82% gc time)
Found contacted branch: [2, 5, 8, 25]
Splitting branch 2 now
Finding connected component
Reassigning contacted branch 2
Splitting branch 5 now
Finding connected component
Reassigning contacted branch 5
Splitting branch 8 now
Finding connected component
Reassigning contacted branch 8
Branch 8 -> 100
Branch 8 -> 101
Splitting branch 25 now
Finding connected component
Reassigning contacted branch 25
Branch 25 -> 102
36.062726 seconds (306.16 k allocations: 101.980 GiB, 9.93% gc time)
Grant domain for each detected cell by watershed
40.807776 seconds (19.30 k allocations: 29.117 GiB, 29.97% gc time)
Drawing longlived_maps
[2, 3, 5, 12, 16, 100, 101, 102]
46.532771 seconds (19.55 k allocations: 33.723 GiB, 27.32% gc time)
tracking cell 1
2.420809 seconds (10.44 M allocations: 2.470 GiB, 54.60% gc time)
Extracting nucleus
11.459096 seconds (1.97 M allocations: 26.490 GiB, 64.47% gc time)
0.670915 seconds (3.08 k allocations: 3.805 GiB, 2.43% gc time)
tracking cell 2
2.816821 seconds (17.18 M allocations: 3.273 GiB, 40.15% gc time)
Extracting nucleus
11.718481 seconds (1.98 M allocations: 26.781 GiB, 65.06% gc time)
0.719665 seconds (3.10 k allocations: 3.800 GiB, 1.88% gc time)
tracking cell 3
2.188970 seconds (15.38 M allocations: 3.059 GiB, 37.42% gc time)
Extracting nucleus
13.213352 seconds (1.97 M allocations: 26.664 GiB, 68.17% gc time)
0.679264 seconds (3.08 k allocations: 3.801 GiB, 2.04% gc time)
tracking cell 4
2.000793 seconds (10.51 M allocations: 2.478 GiB, 24.67% gc time)
Extracting nucleus
11.950444 seconds (1.98 M allocations: 26.638 GiB, 67.35% gc time)
0.842101 seconds (3.10 k allocations: 3.793 GiB, 1.08% gc time)
tracking cell 5
2.386857 seconds (14.36 M allocations: 2.937 GiB, 41.96% gc time)
Extracting nucleus
11.581298 seconds (1.98 M allocations: 26.638 GiB, 63.95% gc time)
0.648292 seconds (3.10 k allocations: 3.809 GiB, 2.11% gc time)
tracking cell 6
3.288837 seconds (19.68 M allocations: 3.572 GiB, 41.40% gc time)
Extracting nucleus
11.397351 seconds (1.97 M allocations: 26.677 GiB, 66.59% gc time)
0.644207 seconds (3.07 k allocations: 3.777 GiB, 1.98% gc time)
tracking cell 7
3.533460 seconds (18.97 M allocations: 3.486 GiB, 41.89% gc time)
Extracting nucleus
13.677638 seconds (1.97 M allocations: 26.636 GiB, 72.27% gc time)
0.822569 seconds (3.07 k allocations: 3.787 GiB, 1.53% gc time)
tracking cell 8
3.898918 seconds (20.01 M allocations: 3.610 GiB, 38.82% gc time)
Extracting nucleus
10.751145 seconds (1.97 M allocations: 26.577 GiB, 64.36% gc time)
0.637901 seconds (3.06 k allocations: 3.812 GiB, 1.94% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T08:44:43.689 Loading 28
216.485274 seconds (24.07 k allocations: 34.506 GiB, 0.16% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
113.197713 seconds (332.34 M allocations: 74.404 GiB, 39.40% gc time)
Finding connected component
4.787373 seconds (547 allocations: 4.926 GiB, 0.20% gc time)
Detecting contacted branch
4.913160 seconds (89.49 k allocations: 39.406 GiB, 19.96% gc time)
Found contacted branch: [1, 3, 4, 7, 8, 12]
Splitting branch 1 now
Finding connected component
Reassigning contacted branch 1
Branch 1 -> 100
Splitting branch 3 now
Finding connected component
Reassigning contacted branch 3
Branch 3 -> 101
Splitting branch 4 now
Finding connected component
Reassigning contacted branch 4
Branch 4 -> 102
Splitting branch 7 now
Finding connected component
Reassigning contacted branch 7
Splitting branch 8 now
Finding connected component
Reassigning contacted branch 8
Branch 8 -> 103
Splitting branch 12 now
Finding connected component
Reassigning contacted branch 12
Branch 12 -> 104
61.479913 seconds (172.68 k allocations: 140.648 GiB, 7.98% gc time)
Grant domain for each detected cell by watershed
42.647809 seconds (19.73 k allocations: 29.092 GiB, 28.34% gc time)
Drawing longlived_maps
[7, 11, 26, 100, 101, 102, 103, 104]
47.756175 seconds (19.98 k allocations: 33.697 GiB, 25.33% gc time)
tracking cell 1
4.848228 seconds (18.77 M allocations: 3.463 GiB, 58.25% gc time)
Extracting nucleus
11.465468 seconds (1.98 M allocations: 26.740 GiB, 63.31% gc time)
0.835470 seconds (3.10 k allocations: 3.781 GiB, 1.57% gc time)
tracking cell 2
1.448403 seconds (7.45 M allocations: 2.114 GiB, 23.54% gc time)
Extracting nucleus
11.136155 seconds (1.98 M allocations: 26.451 GiB, 64.53% gc time)
0.669572 seconds (3.10 k allocations: 3.854 GiB, 2.07% gc time)
tracking cell 3
1.741709 seconds (10.82 M allocations: 2.515 GiB, 30.09% gc time)
Extracting nucleus
13.227158 seconds (1.97 M allocations: 26.487 GiB, 72.32% gc time)
0.632217 seconds (3.06 k allocations: 3.782 GiB, 2.08% gc time)
tracking cell 4
5.374227 seconds (27.93 M allocations: 4.555 GiB, 46.31% gc time)
Extracting nucleus
10.600052 seconds (1.98 M allocations: 26.912 GiB, 60.12% gc time)
0.836337 seconds (3.10 k allocations: 3.841 GiB, 1.62% gc time)
tracking cell 5
6.055156 seconds (28.47 M allocations: 4.619 GiB, 39.13% gc time)
Extracting nucleus
10.286433 seconds (1.98 M allocations: 26.921 GiB, 57.84% gc time)
0.841117 seconds (3.10 k allocations: 3.830 GiB, 1.60% gc time)
tracking cell 6
2.511816 seconds (16.52 M allocations: 3.194 GiB, 38.07% gc time)
Extracting nucleus
12.346421 seconds (1.98 M allocations: 26.684 GiB, 69.68% gc time)
0.707333 seconds (3.09 k allocations: 3.821 GiB, 2.47% gc time)
tracking cell 7
3.767720 seconds (20.57 M allocations: 3.677 GiB, 43.52% gc time)
Extracting nucleus
10.273931 seconds (1.98 M allocations: 26.830 GiB, 60.05% gc time)
0.663290 seconds (3.10 k allocations: 3.803 GiB, 2.01% gc time)
tracking cell 8
2.944323 seconds (16.73 M allocations: 3.219 GiB, 41.17% gc time)
Extracting nucleus
16.689331 seconds (1.97 M allocations: 26.618 GiB, 76.06% gc time)
0.853558 seconds (3.08 k allocations: 3.809 GiB, 1.51% gc time)
real 48m31.056s
user 665m56.702s
sys 46m10.771s
Processing /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200314, output /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200314_result/output
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T08:57:30.852 Loading 29
224.096476 seconds (3.42 M allocations: 34.673 GiB, 0.44% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
137.647233 seconds (348.14 M allocations: 75.175 GiB, 37.94% gc time)
Finding connected component
5.426606 seconds (179.91 k allocations: 4.934 GiB, 0.19% gc time)
Detecting contacted branch
3.674742 seconds (1.18 M allocations: 9.904 GiB, 17.47% gc time)
Found contacted branch: [4]
Splitting branch 4 now
Finding connected component
Reassigning contacted branch 4
13.615788 seconds (3.64 M allocations: 26.883 GiB, 10.10% gc time)
Grant domain for each detected cell by watershed
46.375321 seconds (1.81 M allocations: 29.753 GiB, 28.00% gc time)
Drawing longlived_maps
[4, 21]
53.000879 seconds (1.90 M allocations: 34.362 GiB, 25.45% gc time)
tracking cell 1
5.377031 seconds (17.70 M allocations: 3.303 GiB, 57.86% gc time)
Extracting nucleus
17.449351 seconds (8.86 M allocations: 27.031 GiB, 54.10% gc time)
3.274389 seconds (2.75 M allocations: 3.920 GiB, 38.57% gc time)
tracking cell 2
3.365617 seconds (16.55 M allocations: 3.199 GiB, 27.42% gc time)
Extracting nucleus
15.729751 seconds (1.97 M allocations: 26.559 GiB, 70.42% gc time)
1.209215 seconds (3.07 k allocations: 3.782 GiB, 1.28% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T09:06:19.605 Loading 30
215.468468 seconds (2.02 M allocations: 34.597 GiB, 0.19% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
105.788192 seconds (332.17 M allocations: 74.402 GiB, 39.81% gc time)
Finding connected component
5.217922 seconds (601 allocations: 4.926 GiB, 0.18% gc time)
Detecting contacted branch
5.960945 seconds (98.09 k allocations: 44.333 GiB, 36.34% gc time)
Found contacted branch: [3, 5, 8, 11]
Splitting branch 3 now
Finding connected component
Reassigning contacted branch 3
Branch 3 -> 100
Splitting branch 5 now
Finding connected component
Reassigning contacted branch 5
Branch 5 -> 101
Splitting branch 8 now
Finding connected component
Reassigning contacted branch 8
Branch 8 -> 102
Branch 8 -> 103
Splitting branch 11 now
Finding connected component
Reassigning contacted branch 11
Branch 11 -> 104
48.524981 seconds (265.96 k allocations: 111.832 GiB, 11.52% gc time)
Grant domain for each detected cell by watershed
46.425724 seconds (20.65 k allocations: 28.025 GiB, 32.52% gc time)
Drawing longlived_maps
[1, 4, 6, 10, 47, 100, 101, 102, 103, 104]
52.999838 seconds (20.90 k allocations: 32.630 GiB, 29.42% gc time)
tracking cell 1
3.405224 seconds (12.20 M allocations: 2.680 GiB, 50.39% gc time)
Extracting nucleus
11.053275 seconds (1.98 M allocations: 26.620 GiB, 59.05% gc time)
0.858782 seconds (3.10 k allocations: 3.778 GiB, 1.55% gc time)
tracking cell 2
3.376698 seconds (18.53 M allocations: 3.434 GiB, 38.45% gc time)
Extracting nucleus
12.203881 seconds (1.98 M allocations: 26.832 GiB, 61.10% gc time)
0.673550 seconds (3.10 k allocations: 3.795 GiB, 1.83% gc time)
tracking cell 3
2.830842 seconds (16.97 M allocations: 3.249 GiB, 35.22% gc time)
Extracting nucleus
12.319306 seconds (1.98 M allocations: 26.780 GiB, 60.30% gc time)
0.840298 seconds (3.10 k allocations: 3.785 GiB, 1.53% gc time)
tracking cell 4
4.067271 seconds (20.07 M allocations: 3.618 GiB, 40.02% gc time)
Extracting nucleus
10.517869 seconds (1.98 M allocations: 26.845 GiB, 55.24% gc time)
0.641547 seconds (3.10 k allocations: 3.813 GiB, 1.75% gc time)
tracking cell 5
2.387584 seconds (11.89 M allocations: 2.643 GiB, 23.68% gc time)
Extracting nucleus
14.225660 seconds (1.97 M allocations: 26.448 GiB, 68.13% gc time)
0.760221 seconds (3.07 k allocations: 3.789 GiB, 1.76% gc time)
tracking cell 6
4.007981 seconds (19.16 M allocations: 3.510 GiB, 37.37% gc time)
Extracting nucleus
11.877638 seconds (1.98 M allocations: 26.836 GiB, 60.35% gc time)
0.835280 seconds (3.10 k allocations: 3.813 GiB, 1.59% gc time)
tracking cell 7
4.451049 seconds (23.19 M allocations: 3.989 GiB, 41.25% gc time)
Extracting nucleus
13.138192 seconds (1.98 M allocations: 26.816 GiB, 63.68% gc time)
0.649172 seconds (3.10 k allocations: 3.823 GiB, 1.81% gc time)
tracking cell 8
3.732088 seconds (20.81 M allocations: 3.706 GiB, 34.34% gc time)
Extracting nucleus
14.902973 seconds (1.98 M allocations: 26.844 GiB, 66.95% gc time)
0.651387 seconds (3.10 k allocations: 3.823 GiB, 1.80% gc time)
tracking cell 9
2.967927 seconds (16.25 M allocations: 3.163 GiB, 40.03% gc time)
Extracting nucleus
12.284779 seconds (1.98 M allocations: 26.690 GiB, 63.23% gc time)
0.697614 seconds (3.10 k allocations: 3.815 GiB, 1.87% gc time)
tracking cell 10
3.932217 seconds (18.08 M allocations: 3.381 GiB, 36.84% gc time)
Extracting nucleus
13.319187 seconds (1.98 M allocations: 26.697 GiB, 65.09% gc time)
0.877252 seconds (3.10 k allocations: 3.834 GiB, 1.49% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T09:19:32.188 Loading 31
215.179936 seconds (24.07 k allocations: 34.506 GiB, 0.16% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
121.976479 seconds (332.40 M allocations: 74.405 GiB, 39.29% gc time)
Finding connected component
4.825011 seconds (661 allocations: 4.926 GiB, 0.23% gc time)
Detecting contacted branch
3.813172 seconds (65.52 k allocations: 24.631 GiB, 19.44% gc time)
Found contacted branch: [5, 7, 30]
Splitting branch 5 now
Finding connected component
Reassigning contacted branch 5
Branch 5 -> 100
Branch 5 -> 101
Splitting branch 7 now
Finding connected component
Reassigning contacted branch 7
Branch 7 -> 102
Splitting branch 30 now
Finding connected component
Reassigning contacted branch 30
30.835923 seconds (4.18 M allocations: 75.314 GiB, 7.65% gc time)
Grant domain for each detected cell by watershed
38.749532 seconds (21.57 k allocations: 28.181 GiB, 33.25% gc time)
Drawing longlived_maps
[1, 30, 36, 100, 101, 102]
43.422338 seconds (21.82 k allocations: 32.786 GiB, 29.68% gc time)
tracking cell 1
3.515687 seconds (13.47 M allocations: 2.831 GiB, 54.64% gc time)
Extracting nucleus
9.717551 seconds (1.98 M allocations: 26.721 GiB, 59.04% gc time)
0.677019 seconds (3.09 k allocations: 3.789 GiB, 2.23% gc time)
tracking cell 2
1.860135 seconds (10.41 M allocations: 2.466 GiB, 36.87% gc time)
Extracting nucleus
11.972035 seconds (1.97 M allocations: 26.549 GiB, 69.92% gc time)
0.746038 seconds (3.07 k allocations: 3.781 GiB, 1.64% gc time)
tracking cell 3
3.504510 seconds (18.25 M allocations: 3.401 GiB, 28.86% gc time)
Extracting nucleus
13.092459 seconds (1.97 M allocations: 26.556 GiB, 71.29% gc time)
0.609417 seconds (3.07 k allocations: 3.790 GiB, 2.03% gc time)
tracking cell 4
3.691624 seconds (17.41 M allocations: 3.301 GiB, 36.56% gc time)
Extracting nucleus
12.348547 seconds (1.98 M allocations: 26.763 GiB, 63.51% gc time)
0.713099 seconds (3.10 k allocations: 3.803 GiB, 1.88% gc time)
tracking cell 5
2.793784 seconds (17.87 M allocations: 3.356 GiB, 45.19% gc time)
Extracting nucleus
12.423879 seconds (1.97 M allocations: 26.690 GiB, 64.93% gc time)
0.647089 seconds (3.09 k allocations: 3.816 GiB, 2.06% gc time)
tracking cell 6
2.462277 seconds (13.11 M allocations: 2.788 GiB, 37.24% gc time)
Extracting nucleus
11.032531 seconds (1.97 M allocations: 26.602 GiB, 61.52% gc time)
0.862483 seconds (3.08 k allocations: 3.795 GiB, 1.49% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T09:29:55.097 Loading 32
210.714864 seconds (24.07 k allocations: 34.506 GiB, 0.17% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
103.018721 seconds (332.35 M allocations: 74.404 GiB, 42.90% gc time)
Finding connected component
5.325411 seconds (483 allocations: 4.925 GiB, 0.17% gc time)
Detecting contacted branch
3.915152 seconds (81.16 k allocations: 34.481 GiB, 19.71% gc time)
Found contacted branch: [2, 3, 6]
Splitting branch 2 now
Finding connected component
Reassigning contacted branch 2
Branch 2 -> 100
Splitting branch 3 now
Finding connected component
Reassigning contacted branch 3
Splitting branch 6 now
Finding connected component
Reassigning contacted branch 6
25.561178 seconds (103.88 k allocations: 85.102 GiB, 10.55% gc time)
Grant domain for each detected cell by watershed
45.292714 seconds (18.75 k allocations: 29.147 GiB, 28.60% gc time)
Drawing longlived_maps
[3, 5, 6, 9, 15, 24, 100]
50.401378 seconds (19.00 k allocations: 33.752 GiB, 26.65% gc time)
tracking cell 1
2.468166 seconds (9.39 M allocations: 2.345 GiB, 44.99% gc time)
Extracting nucleus
10.812532 seconds (1.98 M allocations: 26.492 GiB, 64.71% gc time)
0.845748 seconds (3.10 k allocations: 3.806 GiB, 1.55% gc time)
tracking cell 2
3.610088 seconds (18.49 M allocations: 3.429 GiB, 37.01% gc time)
Extracting nucleus
11.286194 seconds (1.98 M allocations: 26.757 GiB, 63.40% gc time)
0.693705 seconds (3.10 k allocations: 3.814 GiB, 1.87% gc time)
tracking cell 3
3.265099 seconds (21.78 M allocations: 3.821 GiB, 40.65% gc time)
Extracting nucleus
10.813411 seconds (1.98 M allocations: 26.773 GiB, 59.69% gc time)
0.686829 seconds (3.09 k allocations: 3.888 GiB, 2.17% gc time)
tracking cell 4
4.250997 seconds (22.69 M allocations: 3.930 GiB, 44.81% gc time)
Extracting nucleus
12.549993 seconds (1.98 M allocations: 26.863 GiB, 63.90% gc time)
1.724136 seconds (3.09 k allocations: 3.792 GiB, 0.76% gc time)
tracking cell 5
2.862154 seconds (17.68 M allocations: 3.333 GiB, 39.11% gc time)
Extracting nucleus
11.342348 seconds (1.98 M allocations: 26.697 GiB, 62.14% gc time)
0.743889 seconds (3.10 k allocations: 3.897 GiB, 2.29% gc time)
tracking cell 6
2.443204 seconds (14.70 M allocations: 2.978 GiB, 36.42% gc time)
Extracting nucleus
11.076907 seconds (1.97 M allocations: 26.511 GiB, 67.30% gc time)
0.690229 seconds (3.07 k allocations: 3.809 GiB, 1.83% gc time)
tracking cell 7
4.401834 seconds (23.90 M allocations: 4.075 GiB, 42.45% gc time)
Extracting nucleus
11.137743 seconds (1.98 M allocations: 26.849 GiB, 57.75% gc time)
0.672951 seconds (3.10 k allocations: 3.802 GiB, 2.31% gc time)
real 43m43.268s
user 607m10.399s
sys 42m52.662s
Processing /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200314, output /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200314_result/output
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T09:41:14.3 Loading 33
211.347211 seconds (3.42 M allocations: 34.673 GiB, 0.42% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
120.624795 seconds (348.12 M allocations: 75.175 GiB, 37.55% gc time)
Finding connected component
6.610012 seconds (179.85 k allocations: 4.934 GiB, 0.20% gc time)
Detecting contacted branch
5.400828 seconds (1.26 M allocations: 39.457 GiB, 16.01% gc time)
Found contacted branch: [2, 10]
Splitting branch 2 now
Finding connected component
Reassigning contacted branch 2
Splitting branch 10 now
Finding connected component
Reassigning contacted branch 10
Branch 10 -> 100
27.256713 seconds (3.81 M allocations: 73.314 GiB, 9.36% gc time)
Grant domain for each detected cell by watershed
44.681745 seconds (1.81 M allocations: 28.630 GiB, 29.91% gc time)
Drawing longlived_maps
[2, 8, 9, 11, 12, 22, 26, 100]
51.273699 seconds (1.90 M allocations: 33.239 GiB, 27.03% gc time)
tracking cell 1
7.014427 seconds (24.25 M allocations: 4.084 GiB, 51.18% gc time)
Extracting nucleus
16.786828 seconds (8.86 M allocations: 27.192 GiB, 52.45% gc time)
2.092058 seconds (2.75 M allocations: 3.954 GiB, 2.25% gc time)
tracking cell 2
2.873322 seconds (15.72 M allocations: 3.100 GiB, 35.30% gc time)
Extracting nucleus
12.441403 seconds (1.98 M allocations: 26.743 GiB, 59.78% gc time)
1.227535 seconds (3.10 k allocations: 3.792 GiB, 1.28% gc time)
tracking cell 3
3.303043 seconds (17.02 M allocations: 3.254 GiB, 38.13% gc time)
Extracting nucleus
13.445754 seconds (1.98 M allocations: 26.760 GiB, 66.62% gc time)
1.266282 seconds (3.10 k allocations: 3.805 GiB, 0.94% gc time)
tracking cell 4
4.009539 seconds (19.06 M allocations: 3.497 GiB, 35.16% gc time)
Extracting nucleus
10.841202 seconds (1.98 M allocations: 26.820 GiB, 56.46% gc time)
1.157626 seconds (3.10 k allocations: 3.791 GiB, 1.13% gc time)
tracking cell 5
3.922714 seconds (18.85 M allocations: 3.473 GiB, 32.73% gc time)
Extracting nucleus
14.341151 seconds (1.98 M allocations: 26.783 GiB, 67.42% gc time)
1.175103 seconds (3.10 k allocations: 3.797 GiB, 1.21% gc time)
tracking cell 6
2.822639 seconds (15.66 M allocations: 3.093 GiB, 38.06% gc time)
Extracting nucleus
14.152973 seconds (1.97 M allocations: 26.657 GiB, 68.62% gc time)
1.191725 seconds (3.09 k allocations: 3.788 GiB, 1.00% gc time)
tracking cell 7
2.644138 seconds (13.71 M allocations: 2.860 GiB, 24.67% gc time)
Extracting nucleus
12.691419 seconds (1.97 M allocations: 26.622 GiB, 65.72% gc time)
1.253361 seconds (3.08 k allocations: 3.791 GiB, 1.06% gc time)
tracking cell 8
6.459914 seconds (26.11 M allocations: 4.338 GiB, 44.88% gc time)
Extracting nucleus
11.660058 seconds (1.98 M allocations: 26.895 GiB, 59.68% gc time)
1.222798 seconds (3.10 k allocations: 3.842 GiB, 1.18% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T09:53:27.244 Loading 34
217.233061 seconds (2.02 M allocations: 34.597 GiB, 0.18% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
120.076821 seconds (332.29 M allocations: 74.404 GiB, 39.29% gc time)
Finding connected component
4.730220 seconds (501 allocations: 4.925 GiB, 0.19% gc time)
Detecting contacted branch
4.618055 seconds (72.88 k allocations: 29.555 GiB, 37.74% gc time)
Found contacted branch: [1, 2, 29]
Splitting branch 1 now
Finding connected component
Reassigning contacted branch 1
Splitting branch 2 now
Finding connected component
Reassigning contacted branch 2
Splitting branch 29 now
Finding connected component
Reassigning contacted branch 29
29.044718 seconds (84.80 k allocations: 80.175 GiB, 12.44% gc time)
Grant domain for each detected cell by watershed
45.424712 seconds (18.45 k allocations: 29.267 GiB, 28.96% gc time)
Drawing longlived_maps
[1, 2, 5, 7, 29, 32]
50.418656 seconds (18.69 k allocations: 33.873 GiB, 27.04% gc time)
tracking cell 1
2.286293 seconds (6.16 M allocations: 1.960 GiB, 45.39% gc time)
Extracting nucleus
11.833255 seconds (1.97 M allocations: 26.385 GiB, 63.70% gc time)
0.879398 seconds (3.10 k allocations: 3.896 GiB, 1.34% gc time)
tracking cell 2
4.718342 seconds (21.26 M allocations: 3.760 GiB, 35.54% gc time)
Extracting nucleus
11.729951 seconds (1.98 M allocations: 26.848 GiB, 63.09% gc time)
0.832980 seconds (3.10 k allocations: 3.795 GiB, 1.62% gc time)
tracking cell 3
6.036995 seconds (27.87 M allocations: 4.548 GiB, 38.96% gc time)
Extracting nucleus
12.749961 seconds (1.98 M allocations: 26.915 GiB, 62.94% gc time)
1.177391 seconds (3.10 k allocations: 3.804 GiB, 1.09% gc time)
tracking cell 4
5.258966 seconds (27.79 M allocations: 4.538 GiB, 45.35% gc time)
Extracting nucleus
10.515440 seconds (1.98 M allocations: 26.908 GiB, 60.46% gc time)
1.314280 seconds (3.09 k allocations: 3.793 GiB, 1.00% gc time)
tracking cell 5
1.790575 seconds (10.90 M allocations: 2.525 GiB, 25.52% gc time)
Extracting nucleus
13.160925 seconds (1.97 M allocations: 26.483 GiB, 69.40% gc time)
0.654308 seconds (3.07 k allocations: 3.802 GiB, 1.84% gc time)
tracking cell 6
2.413919 seconds (13.29 M allocations: 2.809 GiB, 25.12% gc time)
Extracting nucleus
12.272405 seconds (1.97 M allocations: 26.502 GiB, 67.75% gc time)
0.649276 seconds (3.06 k allocations: 3.782 GiB, 1.99% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T10:04:06.614 Loading 35
217.455933 seconds (24.07 k allocations: 34.506 GiB, 0.16% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
116.667229 seconds (332.29 M allocations: 74.404 GiB, 38.35% gc time)
Finding connected component
5.005540 seconds (544 allocations: 4.926 GiB, 0.20% gc time)
Detecting contacted branch
4.234205 seconds (73.22 k allocations: 29.556 GiB, 19.86% gc time)
Found contacted branch: [1, 6, 9, 21, 35]
Splitting branch 1 now
Finding connected component
Reassigning contacted branch 1
Splitting branch 6 now
Finding connected component
Reassigning contacted branch 6
Branch 6 -> 100
Splitting branch 9 now
Finding connected component
Reassigning contacted branch 9
Branch 9 -> 101
Splitting branch 21 now
Finding connected component
Reassigning contacted branch 21
Splitting branch 35 now
Finding connected component
Reassigning contacted branch 35
43.917739 seconds (120.27 k allocations: 113.925 GiB, 9.24% gc time)
Grant domain for each detected cell by watershed
38.732629 seconds (19.98 k allocations: 28.311 GiB, 33.21% gc time)
Drawing longlived_maps
[1, 13, 21, 35, 100, 101]
43.899685 seconds (20.22 k allocations: 32.916 GiB, 30.65% gc time)
tracking cell 1
2.507008 seconds (11.18 M allocations: 2.558 GiB, 48.17% gc time)
Extracting nucleus
14.788179 seconds (1.97 M allocations: 26.477 GiB, 73.26% gc time)
0.877126 seconds (3.08 k allocations: 3.885 GiB, 1.64% gc time)
tracking cell 2
3.464489 seconds (19.41 M allocations: 3.539 GiB, 43.79% gc time)
Extracting nucleus
9.960650 seconds (1.98 M allocations: 26.836 GiB, 56.81% gc time)
0.640406 seconds (3.09 k allocations: 3.795 GiB, 2.16% gc time)
tracking cell 3
3.123146 seconds (18.63 M allocations: 3.446 GiB, 42.09% gc time)
Extracting nucleus
11.082292 seconds (1.98 M allocations: 26.717 GiB, 65.31% gc time)
0.675912 seconds (3.09 k allocations: 3.823 GiB, 2.25% gc time)
tracking cell 4
4.429925 seconds (20.39 M allocations: 3.655 GiB, 40.85% gc time)
Extracting nucleus
11.120494 seconds (1.97 M allocations: 26.612 GiB, 64.08% gc time)
0.661033 seconds (3.07 k allocations: 3.819 GiB, 2.08% gc time)
tracking cell 5
7.819241 seconds (30.41 M allocations: 4.851 GiB, 40.99% gc time)
Extracting nucleus
9.316150 seconds (1.98 M allocations: 26.925 GiB, 55.01% gc time)
0.653050 seconds (3.10 k allocations: 3.881 GiB, 2.16% gc time)
tracking cell 6
4.018884 seconds (20.61 M allocations: 3.682 GiB, 43.49% gc time)
Extracting nucleus
10.918761 seconds (1.98 M allocations: 26.791 GiB, 64.58% gc time)
0.840517 seconds (3.09 k allocations: 3.810 GiB, 1.64% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T10:14:53.149 Loading 36
216.736212 seconds (24.07 k allocations: 34.506 GiB, 0.16% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
128.783158 seconds (332.43 M allocations: 74.406 GiB, 38.06% gc time)
Finding connected component
4.982159 seconds (606 allocations: 4.925 GiB, 0.18% gc time)
Detecting contacted branch
3.470684 seconds (57.61 k allocations: 19.705 GiB, 21.01% gc time)
Found contacted branch: [11]
Splitting branch 11 now
Finding connected component
Reassigning contacted branch 11
Branch 11 -> 100
13.291397 seconds (63.37 k allocations: 36.579 GiB, 8.63% gc time)
Grant domain for each detected cell by watershed
44.138803 seconds (18.65 k allocations: 28.781 GiB, 27.25% gc time)
Drawing longlived_maps
[5, 9, 12, 100]
49.467101 seconds (18.89 k allocations: 33.386 GiB, 25.32% gc time)
tracking cell 1
7.054021 seconds (26.34 M allocations: 4.366 GiB, 61.54% gc time)
Extracting nucleus
9.258094 seconds (1.98 M allocations: 26.884 GiB, 53.37% gc time)
0.833370 seconds (3.10 k allocations: 3.817 GiB, 1.47% gc time)
tracking cell 2
5.104728 seconds (24.84 M allocations: 4.187 GiB, 43.26% gc time)
Extracting nucleus
10.235306 seconds (1.98 M allocations: 26.899 GiB, 58.63% gc time)
0.872581 seconds (3.10 k allocations: 3.796 GiB, 1.46% gc time)
tracking cell 3
3.118058 seconds (19.33 M allocations: 3.529 GiB, 36.50% gc time)
Extracting nucleus
11.277152 seconds (1.98 M allocations: 26.789 GiB, 63.54% gc time)
0.676831 seconds (3.10 k allocations: 3.825 GiB, 2.13% gc time)
tracking cell 4
3.593011 seconds (18.88 M allocations: 3.476 GiB, 41.12% gc time)
Extracting nucleus
11.875325 seconds (1.97 M allocations: 26.754 GiB, 62.91% gc time)
0.643481 seconds (3.08 k allocations: 3.806 GiB, 2.09% gc time)
real 43m33.304s
user 615m49.555s
sys 42m51.892s
Computing file changes ...
