test22.log.2
Processing /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322, output /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322_result/output
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T15:25:30.255 Loading 21
353.281375 seconds (1.08 M allocations: 29.496 GiB, 0.56% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
158.051829 seconds (325.64 M allocations: 86.043 GiB, 38.35% gc time)
Finding connected component
7.800242 seconds (180.02 k allocations: 6.312 GiB, 0.21% gc time)
No longlived cells found, skipping
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T15:34:10.018 Loading 22
352.366906 seconds (34.20 k allocations: 29.446 GiB, 0.95% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
169.123332 seconds (309.63 M allocations: 85.265 GiB, 37.46% gc time)
Finding connected component
7.811103 seconds (475 allocations: 6.304 GiB, 1.45% gc time)
Detecting contacted branch
5.973193 seconds (1.24 M allocations: 18.969 GiB, 18.35% gc time)
Found contacted branch: [13]
Splitting branch 13 now
Finding connected component
Reassigning contacted branch 13
22.795024 seconds (3.70 M allocations: 40.672 GiB, 10.31% gc time)
Grant domain for each detected cell by watershed
71.472388 seconds (1.84 M allocations: 37.024 GiB, 27.72% gc time)
Drawing longlived_maps
[12, 13, 30]
85.132260 seconds (1.87 M allocations: 42.919 GiB, 23.31% gc time)
tracking cell 1
11.399651 seconds (27.26 M allocations: 4.785 GiB, 58.05% gc time)
Extracting nucleus
20.822550 seconds (9.75 M allocations: 34.491 GiB, 54.46% gc time)
2.747179 seconds (2.76 M allocations: 4.957 GiB, 2.57% gc time)
tracking cell 2
3.797057 seconds (15.57 M allocations: 3.423 GiB, 37.85% gc time)
Extracting nucleus
41.153489 seconds (2.53 M allocations: 33.932 GiB, 82.54% gc time)
2.122687 seconds (3.81 k allocations: 4.845 GiB, 1.71% gc time)
tracking cell 3
5.376988 seconds (17.47 M allocations: 3.650 GiB, 35.67% gc time)
Extracting nucleus
23.568921 seconds (2.53 M allocations: 33.916 GiB, 70.58% gc time)
1.937610 seconds (3.80 k allocations: 4.845 GiB, 1.37% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T15:48:39.534 Loading 23
400.285181 seconds (34.20 k allocations: 29.446 GiB, 0.73% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
112.506338 seconds (309.52 M allocations: 85.263 GiB, 47.52% gc time)
Finding connected component
7.368465 seconds (480 allocations: 6.304 GiB, 0.16% gc time)
Detecting contacted branch
3.989313 seconds (42.69 k allocations: 6.309 GiB, 16.93% gc time)
Found contacted branch: [4]
Splitting branch 4 now
Finding connected component
Reassigning contacted branch 4
Branch 4 -> 100
19.760729 seconds (130.86 k allocations: 27.911 GiB, 8.76% gc time)
Grant domain for each detected cell by watershed
68.572342 seconds (21.20 k allocations: 36.235 GiB, 28.34% gc time)
Drawing longlived_maps
[100]
83.290533 seconds (21.44 k allocations: 42.128 GiB, 24.56% gc time)
tracking cell 1
11.047417 seconds (27.39 M allocations: 4.832 GiB, 55.36% gc time)
Extracting nucleus
19.765976 seconds (2.52 M allocations: 34.030 GiB, 70.23% gc time)
1.034084 seconds (3.79 k allocations: 4.845 GiB, 2.03% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T16:00:14.865 Loading 24
387.285062 seconds (34.20 k allocations: 29.446 GiB, 0.71% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
100.723056 seconds (309.48 M allocations: 85.263 GiB, 45.44% gc time)
Finding connected component
7.483389 seconds (442 allocations: 6.304 GiB, 0.16% gc time)
Detecting contacted branch
4.558187 seconds (52.67 k allocations: 12.613 GiB, 17.08% gc time)
Found contacted branch: [5]
Splitting branch 5 now
Finding connected component
Reassigning contacted branch 5
Branch 5 -> 100
20.539708 seconds (109.70 k allocations: 34.212 GiB, 8.45% gc time)
Grant domain for each detected cell by watershed
67.933759 seconds (23.01 k allocations: 38.305 GiB, 25.64% gc time)
Drawing longlived_maps
[2, 100]
81.266546 seconds (23.24 k allocations: 44.199 GiB, 21.46% gc time)
tracking cell 1
4.796224 seconds (12.80 M allocations: 3.093 GiB, 66.63% gc time)
Extracting nucleus
20.970475 seconds (2.52 M allocations: 33.718 GiB, 70.18% gc time)
1.838399 seconds (3.79 k allocations: 4.917 GiB, 1.07% gc time)
tracking cell 2
7.304642 seconds (26.52 M allocations: 4.728 GiB, 51.33% gc time)
Extracting nucleus
19.715361 seconds (2.52 M allocations: 33.994 GiB, 68.14% gc time)
1.751389 seconds (3.79 k allocations: 4.846 GiB, 1.16% gc time)
real 47m45.600s
user 548m59.768s
sys 50m2.946s
Processing /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322, output /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322_result/output
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T16:13:13.072 Loading 25
363.645073 seconds (1.08 M allocations: 29.496 GiB, 0.61% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
152.891884 seconds (325.59 M allocations: 86.042 GiB, 42.29% gc time)
Finding connected component
7.631201 seconds (179.94 k allocations: 6.313 GiB, 0.24% gc time)
Detecting contacted branch
5.321116 seconds (1.19 M allocations: 12.663 GiB, 14.42% gc time)
Found contacted branch: [27]
Splitting branch 27 now
Finding connected component
Reassigning contacted branch 27
19.147993 seconds (3.65 M allocations: 34.366 GiB, 8.52% gc time)
Grant domain for each detected cell by watershed
85.150862 seconds (1.84 M allocations: 38.224 GiB, 42.32% gc time)
Drawing longlived_maps
[15, 27]
98.593652 seconds (1.87 M allocations: 44.119 GiB, 36.55% gc time)
tracking cell 1
8.099889 seconds (16.73 M allocations: 3.530 GiB, 59.10% gc time)
Extracting nucleus
25.270179 seconds (9.74 M allocations: 34.128 GiB, 61.75% gc time)
2.865346 seconds (2.76 M allocations: 4.969 GiB, 2.00% gc time)
tracking cell 2
6.574478 seconds (20.03 M allocations: 3.954 GiB, 42.37% gc time)
Extracting nucleus
23.488787 seconds (2.52 M allocations: 33.878 GiB, 70.74% gc time)
1.795815 seconds (3.78 k allocations: 4.875 GiB, 1.08% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T16:26:25.461 Loading 26
612.894134 seconds (34.20 k allocations: 29.446 GiB, 0.53% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
118.424646 seconds (309.57 M allocations: 85.264 GiB, 45.09% gc time)
Finding connected component
8.581059 seconds (412 allocations: 6.304 GiB, 0.16% gc time)
Detecting contacted branch
5.269405 seconds (73.20 k allocations: 25.223 GiB, 16.86% gc time)
Found contacted branch: [3, 4, 6]
Splitting branch 3 now
Finding connected component
Reassigning contacted branch 3
Splitting branch 4 now
Finding connected component
Reassigning contacted branch 4
Branch 4 -> 100
Splitting branch 6 now
Finding connected component
Reassigning contacted branch 6
49.875499 seconds (176.52 k allocations: 90.021 GiB, 10.61% gc time)
Grant domain for each detected cell by watershed
60.565982 seconds (22.75 k allocations: 37.899 GiB, 25.72% gc time)
Drawing longlived_maps
[2, 3, 6, 100]
74.982568 seconds (22.99 k allocations: 43.792 GiB, 21.75% gc time)
tracking cell 1
13.449080 seconds (34.19 M allocations: 5.643 GiB, 58.11% gc time)
Extracting nucleus
20.217665 seconds (2.53 M allocations: 34.427 GiB, 68.47% gc time)
1.808125 seconds (3.84 k allocations: 4.859 GiB, 1.05% gc time)
tracking cell 2
6.877777 seconds (23.00 M allocations: 4.309 GiB, 33.17% gc time)
Extracting nucleus
26.085616 seconds (2.52 M allocations: 33.999 GiB, 73.23% gc time)
1.887119 seconds (3.79 k allocations: 4.869 GiB, 0.99% gc time)
tracking cell 3
5.060386 seconds (18.60 M allocations: 3.784 GiB, 35.06% gc time)
Extracting nucleus
20.413779 seconds (2.52 M allocations: 33.897 GiB, 69.76% gc time)
1.902421 seconds (3.79 k allocations: 4.848 GiB, 1.02% gc time)
tracking cell 4
5.480901 seconds (18.61 M allocations: 3.785 GiB, 34.17% gc time)
Extracting nucleus
22.514247 seconds (2.52 M allocations: 33.854 GiB, 73.00% gc time)
1.942118 seconds (3.78 k allocations: 4.843 GiB, 0.97% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T16:45:25.037 Loading 27
647.372079 seconds (34.20 k allocations: 29.446 GiB, 0.67% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
144.503997 seconds (309.62 M allocations: 85.265 GiB, 39.06% gc time)
Finding connected component
7.635886 seconds (530 allocations: 6.304 GiB, 1.84% gc time)
No longlived cells found, skipping
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T16:58:45.247 Loading 28
706.729143 seconds (34.20 k allocations: 29.446 GiB, 0.40% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
146.582111 seconds (309.64 M allocations: 85.265 GiB, 39.62% gc time)
Finding connected component
7.343466 seconds (500 allocations: 6.304 GiB, 0.19% gc time)
No longlived cells found, skipping
real 60m39.776s
user 524m24.332s
sys 52m30.075s
HDF5-DIAG: Error detected in HDF5 (1.10.4) thread 0:
#000: H5Dio.c line 199 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: H5Dio.c line 601 in H5D__read(): can't read data
major: Dataset
minor: Read failed
#002: H5Dchunk.c line 2229 in H5D__chunk_read(): unable to read raw data chunk
major: Low-level I/O
minor: Read failed
#003: H5Dchunk.c line 3609 in H5D__chunk_lock(): data pipeline read failed
major: Dataset
minor: Filter operation failed
#004: H5Z.c line 1326 in H5Z_pipeline(): filter returned failure during read
major: Data filters
minor: Read failed
#005: H5Zdeflate.c line 123 in H5Z_filter_deflate(): inflate() failed
major: Data filters
minor: Unable to initialize object
ERROR: LoadError: Error reading dataset /DataSet/ResolutionLevel 0/TimePoint 14/Channel 0/Data
Stacktrace:
[1] error(::String, ::String) at ./error.jl:42
[2] h5d_read(::Int64, ::Int64, ::Int64, ::Int64, ::Int64, ::Array{UInt16,3}) at /home/hf/.julia/packages/HDF5/ECBXn/src/HDF5.jl:2304
[3] _getindex(::HDF5Dataset, ::Type{T} where T, ::UnitRange{Int64}, ::Vararg{UnitRange{Int64},N} where N) at /home/hf/.julia/packages/HDF5/ECBXn/src/HDF5.jl:1769
[4] _getindex(::HDF5Dataset, ::UnitRange{Int64}, ::UnitRange{Int64}, ::Vararg{UnitRange{Int64},N} where N) at /home/hf/.julia/packages/HDF5/ECBXn/src/HDF5.jl:1758
[5] getindex(::HDF5Dataset, ::UnitRange{Int64}, ::UnitRange{Int64}, ::UnitRange{Int64}) at /home/hf/.julia/packages/HDF5/ECBXn/src/HDF5.jl:1748
[6] (::var"#32#33"{Int64,Array{Gray{Normed{UInt16,16}},3}})(::HDF5File) at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/julia2ims.jl:151
[7] h5open(::var"#32#33"{Int64,Array{Gray{Normed{UInt16,16}},3}}, ::String; swmr::Bool) at /home/hf/.julia/packages/HDF5/ECBXn/src/HDF5.jl:695
[8] h5open at /home/hf/.julia/packages/HDF5/ECBXn/src/HDF5.jl:693 [inlined]
[9] loadims(::String) at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/julia2ims.jl:148
[10] macro expansion at ./util.jl:175 [inlined]
[11] playing(::Int64) at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/test22.jl:19
[12] top-level scope at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/test22.jl:52
[13] include(::Module, ::String) at ./Base.jl:377
[14] exec_options(::Base.JLOptions) at ./client.jl:288
[15] _start() at ./client.jl:484
in expression starting at /datahub/rawdata/tandeng/mRNA_imaging/CoutingmRNA.jl/test22.jl:51
Processing /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322, output /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322_result/output
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T17:13:51.36 Loading 29
771.842745 seconds (1.08 M allocations: 29.496 GiB, 0.32% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
130.224376 seconds (325.58 M allocations: 86.042 GiB, 41.78% gc time)
Finding connected component
8.227843 seconds (180.00 k allocations: 6.313 GiB, 0.16% gc time)
Detecting contacted branch
5.864771 seconds (1.30 M allocations: 25.276 GiB, 15.71% gc time)
Found contacted branch: Int64[]
6.008328 seconds (1.54 M allocations: 25.288 GiB, 15.41% gc time)
Grant domain for each detected cell by watershed
81.230195 seconds (1.84 M allocations: 37.867 GiB, 41.97% gc time)
Drawing longlived_maps
[6, 7, 9, 42]
95.417644 seconds (1.87 M allocations: 43.762 GiB, 36.51% gc time)
tracking cell 1
13.491902 seconds (34.91 M allocations: 5.696 GiB, 52.94% gc time)
Extracting nucleus
21.180022 seconds (9.76 M allocations: 34.765 GiB, 53.71% gc time)
2.826098 seconds (2.76 M allocations: 4.969 GiB, 2.14% gc time)
tracking cell 2
8.078062 seconds (25.60 M allocations: 4.619 GiB, 46.69% gc time)
Extracting nucleus
19.443686 seconds (2.53 M allocations: 34.178 GiB, 66.37% gc time)
1.940980 seconds (3.81 k allocations: 4.875 GiB, 1.19% gc time)
tracking cell 3
6.900177 seconds (24.93 M allocations: 4.539 GiB, 41.70% gc time)
Extracting nucleus
21.120626 seconds (2.53 M allocations: 34.168 GiB, 70.32% gc time)
1.715008 seconds (3.82 k allocations: 4.860 GiB, 1.05% gc time)
tracking cell 4
4.336873 seconds (17.02 M allocations: 3.596 GiB, 32.48% gc time)
Extracting nucleus
21.359264 seconds (2.52 M allocations: 33.827 GiB, 70.81% gc time)
1.779917 seconds (3.79 k allocations: 4.853 GiB, 1.31% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T17:35:25.602 Loading 30
674.787655 seconds (34.20 k allocations: 29.446 GiB, 0.61% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
137.039720 seconds (309.61 M allocations: 85.265 GiB, 40.78% gc time)
Finding connected component
7.297187 seconds (499 allocations: 6.304 GiB, 0.15% gc time)
Detecting contacted branch
4.639674 seconds (52.82 k allocations: 12.613 GiB, 17.89% gc time)
Found contacted branch: [3, 6]
Splitting branch 3 now
Finding connected component
Reassigning contacted branch 3
Branch 3 -> 100
Splitting branch 6 now
Finding connected component
Reassigning contacted branch 6
35.474949 seconds (2.42 M allocations: 55.908 GiB, 10.59% gc time)
Grant domain for each detected cell by watershed
57.047884 seconds (22.61 k allocations: 38.239 GiB, 25.08% gc time)
Drawing longlived_maps
[6, 100]
71.318758 seconds (22.84 k allocations: 44.133 GiB, 21.04% gc time)
tracking cell 1
10.628504 seconds (34.10 M allocations: 5.633 GiB, 68.16% gc time)
Extracting nucleus
19.505236 seconds (2.53 M allocations: 34.402 GiB, 65.96% gc time)
1.871677 seconds (3.84 k allocations: 4.853 GiB, 0.88% gc time)
tracking cell 2
3.456347 seconds (17.66 M allocations: 3.672 GiB, 46.63% gc time)
Extracting nucleus
22.097527 seconds (2.52 M allocations: 33.784 GiB, 71.93% gc time)
1.857449 seconds (3.77 k allocations: 4.867 GiB, 1.18% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T17:53:08.533 Loading 31
real 41m17.471s
user 336m0.445s
sys 27m38.351s
Processing /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322, output /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322_result/output
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T17:55:10.168 Loading 33
510.897690 seconds (1.08 M allocations: 29.496 GiB, 0.47% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
145.943399 seconds (325.68 M allocations: 86.043 GiB, 39.66% gc time)
Finding connected component
7.659420 seconds (180.04 k allocations: 6.312 GiB, 0.19% gc time)
No longlived cells found, skipping
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T18:06:15.219 Loading 34
353.370059 seconds (34.20 k allocations: 29.446 GiB, 0.72% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
157.490619 seconds (309.69 M allocations: 85.266 GiB, 38.61% gc time)
Finding connected component
7.477124 seconds (374 allocations: 6.303 GiB, 0.25% gc time)
Detecting contacted branch
5.148627 seconds (1.19 M allocations: 12.663 GiB, 14.44% gc time)
Found contacted branch: [3]
Splitting branch 3 now
Finding connected component
Reassigning contacted branch 3
Branch 3 -> 100
20.187937 seconds (4.06 M allocations: 34.375 GiB, 7.87% gc time)
Grant domain for each detected cell by watershed
64.773597 seconds (1.84 M allocations: 38.303 GiB, 24.44% gc time)
Drawing longlived_maps
[2, 100]
79.017720 seconds (1.87 M allocations: 44.197 GiB, 20.83% gc time)
tracking cell 1
13.009723 seconds (38.76 M allocations: 6.155 GiB, 63.86% gc time)
Extracting nucleus
24.280859 seconds (9.75 M allocations: 34.786 GiB, 61.84% gc time)
2.736400 seconds (2.76 M allocations: 4.981 GiB, 1.74% gc time)
tracking cell 2
8.059196 seconds (21.37 M allocations: 4.114 GiB, 42.49% gc time)
Extracting nucleus
26.599463 seconds (2.52 M allocations: 33.867 GiB, 76.14% gc time)
1.815159 seconds (3.77 k allocations: 4.853 GiB, 1.20% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T18:19:11.578 Loading 35
347.803990 seconds (34.20 k allocations: 29.446 GiB, 1.09% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
128.001039 seconds (309.56 M allocations: 85.264 GiB, 41.94% gc time)
Finding connected component
7.426252 seconds (374 allocations: 6.303 GiB, 0.16% gc time)
No longlived cells found, skipping
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T18:27:15.513 Loading 36
359.299897 seconds (34.20 k allocations: 29.446 GiB, 0.84% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
159.815133 seconds (309.66 M allocations: 85.266 GiB, 38.89% gc time)
Finding connected component
7.664618 seconds (418 allocations: 6.303 GiB, 0.17% gc time)
No longlived cells found, skipping
real 41m38.866s
user 424m8.197s
sys 48m39.883s
Processing /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322, output /datahub/rawdata/tandeng/mRNA_imaging/mRNA_confocal_hamamatsu-60X-TIRF/20200322_result/output
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T18:36:47.457 Loading 37
400.203351 seconds (1.08 M allocations: 29.496 GiB, 0.58% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
176.195351 seconds (325.65 M allocations: 86.043 GiB, 39.05% gc time)
Finding connected component
8.297441 seconds (179.92 k allocations: 6.313 GiB, 0.20% gc time)
Detecting contacted branch
4.917415 seconds (1.13 M allocations: 6.356 GiB, 15.47% gc time)
Found contacted branch: Int64[]
5.058247 seconds (1.37 M allocations: 6.367 GiB, 15.04% gc time)
Grant domain for each detected cell by watershed
65.216473 seconds (1.84 M allocations: 38.282 GiB, 26.58% gc time)
Drawing longlived_maps
[24]
79.917529 seconds (1.87 M allocations: 44.177 GiB, 22.63% gc time)
tracking cell 1
10.006787 seconds (20.38 M allocations: 3.964 GiB, 55.67% gc time)
Extracting nucleus
27.115494 seconds (9.74 M allocations: 34.127 GiB, 63.42% gc time)
2.741762 seconds (2.76 M allocations: 4.934 GiB, 2.51% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T18:49:21.119 Loading 38
365.854081 seconds (34.20 k allocations: 29.446 GiB, 1.04% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
156.077204 seconds (309.61 M allocations: 85.265 GiB, 38.14% gc time)
Finding connected component
7.325081 seconds (496 allocations: 6.303 GiB, 0.20% gc time)
No longlived cells found, skipping
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T18:58:10.917 Loading 39
391.717961 seconds (34.20 k allocations: 29.446 GiB, 0.52% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
134.737491 seconds (309.57 M allocations: 85.264 GiB, 42.09% gc time)
Finding connected component
7.825844 seconds (459 allocations: 6.304 GiB, 0.16% gc time)
Detecting contacted branch
4.725279 seconds (52.51 k allocations: 12.613 GiB, 15.83% gc time)
Found contacted branch: Int64[]
4.725471 seconds (52.55 k allocations: 12.613 GiB, 15.83% gc time)
Grant domain for each detected cell by watershed
79.211370 seconds (21.91 k allocations: 38.066 GiB, 32.20% gc time)
Drawing longlived_maps
[1, 17]
94.340269 seconds (22.15 k allocations: 43.960 GiB, 27.80% gc time)
tracking cell 1
5.321442 seconds (16.68 M allocations: 3.555 GiB, 65.57% gc time)
Extracting nucleus
23.054645 seconds (2.52 M allocations: 33.838 GiB, 71.44% gc time)
2.028759 seconds (3.79 k allocations: 4.850 GiB, 0.94% gc time)
tracking cell 2
7.321044 seconds (28.09 M allocations: 4.915 GiB, 55.94% gc time)
Extracting nucleus
19.448984 seconds (2.53 M allocations: 34.079 GiB, 65.40% gc time)
1.826322 seconds (3.80 k allocations: 4.848 GiB, 0.97% gc time)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2020-05-13T19:10:56.551 Loading 40
377.121823 seconds (34.20 k allocations: 29.446 GiB, 0.75% gc time)
Load done
Applying LoG(40) at Maximum Z Projection
Done
153.353818 seconds (309.64 M allocations: 85.265 GiB, 39.23% gc time)
Finding connected component
8.212704 seconds (537 allocations: 6.304 GiB, 0.17% gc time)
Detecting contacted branch
5.412642 seconds (82.10 k allocations: 31.526 GiB, 19.45% gc time)
Found contacted branch: [3, 6, 16, 32]
Splitting branch 3 now
Finding connected component
Reassigning contacted branch 3
Branch 3 -> 100
Splitting branch 6 now
Finding connected component
Reassigning contacted branch 6
Splitting branch 16 now
Finding connected component
Reassigning contacted branch 16
Splitting branch 32 now
Finding connected component
Reassigning contacted branch 32
67.303007 seconds (2.41 M allocations: 118.016 GiB, 11.45% gc time)
Grant domain for each detected cell by watershed
63.091484 seconds (22.93 k allocations: 37.952 GiB, 24.45% gc time)
Drawing longlived_maps
[6, 16, 26, 32, 100]
77.366689 seconds (23.18 k allocations: 43.845 GiB, 20.82% gc time)
tracking cell 1
6.480680 seconds (20.99 M allocations: 4.069 GiB, 59.92% gc time)
Extracting nucleus
25.762757 seconds (2.52 M allocations: 33.967 GiB, 74.46% gc time)
1.755545 seconds (3.79 k allocations: 4.844 GiB, 0.75% gc time)
tracking cell 2
4.272749 seconds (19.51 M allocations: 3.893 GiB, 44.98% gc time)
Extracting nucleus
22.365920 seconds (2.52 M allocations: 33.936 GiB, 71.02% gc time)
1.837936 seconds (3.79 k allocations: 4.849 GiB, 1.14% gc time)
tracking cell 3
3.227450 seconds (15.74 M allocations: 3.444 GiB, 47.88% gc time)
Extracting nucleus
38.512529 seconds (2.52 M allocations: 33.762 GiB, 80.65% gc time)
2.140678 seconds (3.77 k allocations: 4.875 GiB, 0.81% gc time)
tracking cell 4
5.177215 seconds (24.45 M allocations: 4.482 GiB, 50.07% gc time)
Extracting nucleus
19.870585 seconds (2.52 M allocations: 34.026 GiB, 68.53% gc time)
1.851932 seconds (3.80 k allocations: 4.847 GiB, 1.00% gc time)
tracking cell 5
6.024323 seconds (19.45 M allocations: 3.886 GiB, 33.50% gc time)
Extracting nucleus
25.487859 seconds (2.52 M allocations: 33.856 GiB, 74.44% gc time)
1.882116 seconds (3.78 k allocations: 4.832 GiB, 1.11% gc time)
real 51m59.807s
user 629m58.704s
sys 50m21.156s
