FIGURES 3D POUR VISU

Clustering ClusteringAgglomerative, distance DistanceSpeed

with mask 2d obtained with Unet 2d segmentation with threshold of 0.5 for binarization

Fichier de configuration (config_clustering8.yaml)

threshold: 2.1
speed_threshold: 15.0
min_len_souspic: 4
data3D_path: "../../../BIGSF_DATA/Clustering_COHRS/COHRS_10p50_0p00_CUBE_3T2_R2.fit"
data3D_reprojected_path : "../../../BIGSF_DATA/Clustering_COHRS/COHRS_reprojected_Unet_fromCut.fits"
mask_toreproject_data_path: "../../../BIGSF_DATA/Clustering_COHRS/Cut.fits"
clustered_data_folder: "../../../BIGSF_DATA/Clustering_COHRS/data_test8"
skeleton_tool: 
  type : SkeletonFilFinder
distance: 
  type : DistanceSpeed
  #speed_threshold: 15.0
  #coefficient_speed : 1.0
clustering_method: 
  type : ClusteringAgglomerative
  #xi : 0.5
  #eps : 1.0
  #min_samples : 7
  distance_threshold: 15.0
denoising_method: 
  type : NoDenoising
modes : ["3d_skeletons", "2d_skeletons", "all_3d_skeletons"]

---

FIGURES

Avec variation d'opacite sur les squelettes 3d en fonction de l' intensite correspondante

Unet 2D MASK (Obtained with Parameter's Experience 8)

• maskd 2 figure8_ske0

Unet 3D Cube plot (Obtained with Parameter's Experience 8)

• volume 3d data plot way 1_ske0
• volume 3d data plot way 1_ske0 zoom in z
• volule 3d data way 2 figure8_ske0 zoom in z
• volule 3d data way 2 figure8_ske0
• marker 3d data plot 4_ske6

CLASSICAL 2D MASK (Obtained with Parameter's Experience 4)

• maskd 2 figure4_ske6
• zoom on maskd 2 figure4_ske6
• zoom on 3d maskd figure4_ske6

CLASSICAL 3D Cube plot (Obtained with Parameter's Experience 4)

• volule 3d data way 1figure4_ske6
• volume 3d data plot way 2_ske6
• marker 3d data plot 4_ske6

Clustering ClusteringDBSCAN, distance DistanceEuclieanEx

Fichier de configuration (config_clustering2.yaml)

  threshold: 2.4
  speed_threshold: 15.0
  min_len_souspic: 4
  data3D_path: "../../../BIGSF_DATA/Clustering_COHRS/COHRS_10p50_0p00_CUBE_3T2_R2.fit"
  data3D_reprojected_path : "../../../BIGSF_DATA/Clustering_COHRS/COHRS_reprojected_10p50_0p00_CUBE_3T2_R2.fit"
  mask_toreproject_data_path: "../../../BIGSF_DATA/Clustering_COHRS/new_full_mask_002011.fits"
  clustered_data_folder: "../../../BIGSF_DATA/Clustering_COHRS/data_test"
  skeleton_tool: 
    type : SkeletonFilFinder
  distance: 
    type : DistanceEuclieanExp
    speed_threshold: 15.0
  clustering_method: 
    type : ClusteringDBSCAN
    eps : 2.0
    min_samples : 7
  denoising_method: 
    type : NoDenoising
  modes : ["3d_skeletons", "2d_skeletons", "all_3d_skeletons"]

---

FIGURES

• Cube 3D interactif)

Clustering ClusteringDBSCAN, distance DistanceSpeedExp

Fichier de configuration (config_clustering3.yaml)

  threshold: 2.4
  speed_threshold: 15.0
  min_len_souspic: 4
  data3D_path: "../../../BIGSF_DATA/Clustering_COHRS/COHRS_10p50_0p00_CUBE_3T2_R2.fit"
  data3D_reprojected_path: "../../../BIGSF_DATA/Clustering_COHRS/COHRS_reprojected_10p50_0p00_CUBE_3T2_R2.fit"
  mask_toreproject_data_path: "../../../BIGSF_DATA/Clustering_COHRS/new_full_mask_002011.fits"
  clustered_data_folder: "../../../BIGSF_DATA/Clustering_COHRS/data_test3"
  skeleton_tool: 
    type : SkeletonFilFinder
  distance: 
    type : DistanceSpeedExp
    speed_threshold: 15.0
  clustering_method: 
    type : ClusteringDBSCAN
    eps : 2.0
    min_samples : 7
  denoising_method: 
    type : NoDenoising
  modes : ["3d_skeletons", "2d_skeletons", "all_3d_skeletons"]

---

FIGURES

• Cube 3D interactif skeleton 6)
• Cube 3D interactif skeleton 7)
• Cube 3D interactif skeleton 12)

Clustering ClusteringDBSCAN, distance DistanceSpeedExp

Fichier de configuration (config_clustering4.yaml)

threshold: 1.8
speed_threshold: 15.0
min_len_souspic: 4
data3D_path: "../../../BIGSF_DATA/Clustering_COHRS/COHRS_10p50_0p00_CUBE_3T2_R2.fit"
data3D_reprojected_path : "../../../BIGSF_DATA/Clustering_COHRS/COHRS_reprojected_10p50_0p00_CUBE_3T2_R2.fit"
mask_toreproject_data_path: "../../../BIGSF_DATA/Clustering_COHRS/new_full_mask_002011.fits"
clustered_data_folder: "../../../BIGSF_DATA/Clustering_COHRS/data_test4"
skeleton_tool: 
  type : SkeletonFilFinder
distance: 
  type : DistanceSpeedExp
  speed_threshold: 15.0
clustering_method: 
  type : ClusteringDBSCAN
  eps : 2.0
  min_samples : 7
denoising_method: 
  type : NoDenoising
modes : ["3d_skeletons", "2d_skeletons", "all_3d_skeletons"]

---

FIGURES

Avec variation d'opacite sur les squelettes 3d en fonction de l' intensite correspondante

• Cube 3D 4 with opacity and grid interactif skeleton 6)
• Cube 3D interactif skeleton 7)
• Cube 3D interactif skeleton 12)

Avec reafectation des doublons en xy en label sur le nuage le plus petit + opacity varition

enleve la supreposition des squelettes e par label en 2d mais c'est tres arbitraire

• Cube 3D interactif skeleton 6)
• Cube 3D interactif skeleton 7)
• Cube 3D interactif skeleton 12)

formule initiale

• Cube 3D interactif skeleton 6)

• Cube 3D interactif skeleton 7)

• Cube 3D interactif skeleton 12)

• i_skeleton = 6

equivalent plotly plotly script Annie skeleton 6)

• i_skeleton = 7

plotly script Annie skeleton 7)

• i_skeleton = 12

plotly script Annie skeleton 12)

Clustering ClusteringDBSCAN, distance DistanceSpeedExp, subclustering_method:SubClusteringSkimageLabel

Fichier de configuration (config_clustering5.yaml)

 threshold: 1.8
speed_threshold: 15.0
min_len_souspic: 4
data3D_path: "../../../BIGSF_DATA/Clustering_COHRS/COHRS_10p50_0p00_CUBE_3T2_R2.fit"
data3D_reprojected_path : "../../../BIGSF_DATA/Clustering_COHRS/COHRS_reprojected_10p50_0p00_CUBE_3T2_R2.fit"
mask_toreproject_data_path: "../../../BIGSF_DATA/Clustering_COHRS/new_full_mask_002011.fits"
clustered_data_folder: "../../../BIGSF_DATA/Clustering_COHRS/data_test5"
skeleton_tool: 
  type : SkeletonFilFinder
distance: 
  type : DistanceSpeedExp
  speed_threshold: 15.0
clustering_method: 
  type : ClusteringDBSCAN
  eps : 2.0
  min_samples : 7
subclustering_method:
  type : SubClusteringSkimageLabel
  connectivity : 2
  eps : 2.0
  min_samples : 7
denoising_method: 
  type : NoDenoising
modes : ["3d_skeletons", "2d_skeletons", "all_3d_skeletons"]

---

FIGURES (Experiment 5)

• Cube 3D interactif skeleton 6)

• Cube 3D interactif skeleton 7)

• Cube 3D interactif skeleton 12)

• i_skeleton = 6

equivalent plotly plotly script 5 Annie skeleton 6)

• i_skeleton = 7

plotly script Annie skeleton 7)

• i_skeleton = 12

plotly script 5 Annie skeleton 12)