easifish/conf/bigstitcher_config.yml at main · JaneliaSciComp/easifish · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
createDataset:
  classname: net.preibisch.bigstitcher.spark.CreateDataset
  advancedArgs: []

resave:
  classname: net.preibisch.bigstitcher.spark.SparkResaveN5
  advancedArgs:
    - '--compression=Zstandard'
    - '--blockSize=64,64,64'
    - '--blockScale=16,16,8'
    - '--useSharding'

detectInterestPoints:
  classname: net.preibisch.bigstitcher.spark.SparkInterestPointDetection
  advancedArgs:
    - '--channelId=1'
    - '--overlappingOnly'
    - '--onlyCompareOverlapTiles'
    - '--label=beads'
    - '--sigma=4.2'
    - '--threshold=0.008'
    - '--minIntensity=230'
    - '--maxIntensity=1800'
    - '--downsampleXY=2'
    - '--downsampleZ=1'

matchInterestPoints:
  classname: net.preibisch.bigstitcher.spark.SparkGeometricDescriptorMatching
  advancedArgs:
    - '--channelId=1'
    - '--label=beads'
    - '--method=PRECISE_TRANSLATION'
    - '--searchRadius=1000'
    - '--transformationModel=TRANSLATION'
    - '--regularizationModel=NONE'
    # ransacMinInlierRatio: default is 0.1 (10%).
    # Raising to 0.2 ensures at least 1 in 5 candidates are
    # consistent — filters tile pairs that happen to match on noise.
    - '--ransacMinInlierRatio=0.1'
    # More neighbors → more discriminative descriptor, fewer false matches.
    # Default 3 is often fine; 5 helps for dense bead fields.
    # Only supported by PRECISE_TRANSLATION.
    - '--numNeighbors=3'
    # Each bead tries this many top descriptor matches.
    # Higher = more candidates for RANSAC to work with.
    # Default 1 is minimal.
    - '--redundancy=1'
    # The ratio between best and second-best descriptor distance.
    # Lower = more permissive. If you get zero candidates, try 2.0.
    - '--significance=3'

solveIPs: &solveIPsArgs
  classname: net.preibisch.bigstitcher.spark.Solver
  advancedArgs:
    - '--channelId=1'
    - '--label=beads'
    - '--method=TWO_ROUND_SIMPLE'
    - '--preAlign=PREALIGN'
    - '--sourcePoints=IP'
    - '--transformationModel=TRANSLATION'
    - '--lambda=0.1'

stitchPairs:
  classname: net.preibisch.bigstitcher.spark.SparkPairwiseStitching
  advancedArgs:
    - '--channelCombine AVERAGE'
    - '--minR 0.7'
    - '-ds 2,2,1'

solvePairs: &solvePairsArgs
  classname: net.preibisch.bigstitcher.spark.Solver
  advancedArgs:
    - '--method=ONE_ROUND_SIMPLE'
    - '--preAlign NO_PREALIGN'
    - '--sourcePoints=STITCHING'

stitchSolve:
  <<: *solveIPsArgs

duplicateTransformation:
  classname: net.preibisch.bigstitcher.spark.DuplicateTransformation
  advancedArgs:
    - '--duplicateMode=CHANNELS'
    - '--sourceId=1'
    - '--transformationsMode=REPLACE_ALL'

intensityMatch:
  classname: net.preibisch.bigstitcher.spark.SparkIntensityMatching
  advancedArgs:
    - '--numCoefficients=8,8,8'
    - '--renderScale=0.1'
    - '--minThreshold=5'
    - '--maxThreshold=65534'
    - '--method=HISTOGRAM'

intensitySolve:
  classname: net.preibisch.bigstitcher.spark.IntensitySolver
  advancedArgs: []

createContainer:
  classname: net.preibisch.bigstitcher.spark.CreateFusionContainer
  advancedArgs:
    - '--multiRes'
    - '--preserveAnisotropy'
    - '--compressionLevel=5'

fuse:
  classname: net.preibisch.bigstitcher.spark.SparkFusion
  advancedArgs:
    - '--fusionMethod=AFFINE'
    # fusion arg values:AVG_BLEND,CLOSEST_PIXEL_WINS
    - '--fusion=AVG_BLEND'
  useIntensityCoefficients: false