mm3/params_postprocessing.yaml at master · junlabucsd/mm3 · 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
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
###############################################################################
# filtering
###############################################################################
filters:
  cell_generation_index: [1]
    # mother cell: 1

  fovpeak:
    # dictionary format fov: [peak1, peak2, ..., peakN]
    # leave value empty for selection of whole FOV
    # otherwise list of peaks as value
    # leave blank to select all fovs and all peaks

  lineages:
    keep_continuous_only: False
    args:
      min_gen: 3

  cutoffs:
    # keys of this dictionary must map scalar or array of scalars attributes in the Cell class
    sb:
      plo: 2
      phi: 2
      #method: logmean
      #method: mean
      method: median
    tau:
      plo: 1.5
      phi: 4
      #method: median-min
      method: median
      #method: mean

###############################################################################
# computations
###############################################################################
computations:
  min_per_frame: 2.
  um_per_pixel: .11
###############################################################################
# plots
###############################################################################
plots:
  distributions:
    attributes:
      sb:
        label: "$S_b$ $[\\mu m]$"
      sd:
        label: "$S_d$ $[\\mu m]$"
      delta:
        label: "$\\Delta_d$ $[\\mu m]$"
      growth_rate:
        label: "$\\lambda$ $[h^{-1}]$"
        scale: 60.
      tau:
        label: "$\\tau$ $[min]$"
      taucyc_min:
        label: "$\\tau_{cyc}$ $[min]$"
      C_min:
        label: "$C$ $[min]$"
      D_min:
        label: "$D$ $[min]$"
      unit_size:
        label: "$S_{0}$ $[\\mu m]$"

  cross correlations:
    attributes:
      sb:
        label: "$S_b$ $[\\mu m]$"
      sd:
        label: "$S_d$ $[\\mu m]$"
      delta:
        label: "$\\Delta_d$ $[\\mu m]$"
      growth_rate:
        label: "$\\lambda$ $[h^{-1}]$"
        scale: 60.
      tau:
        label: "$\\tau$ $[min]$"
      taucyc_min:
        label: "$\\tau_{cyc}$ $[min]$"
      C_min:
        label: "$C$ $[min]$"
      D_min:
        label: "$D$ $[min]$"
      unit_size:
        label: "$S_{0}$ $[\\mu m]$"
    args:
      method: pearsonr
      #method: spearmanr

  autocorrelations:
    attributes:
      sb:
        label_d: "$S_b^{n+1}$ $[\\mu m]$"
        label_m: "$S_b^{n}$ $[\\mu m]$"
      sd:
        label_d: "$S_d^{n+1}$ $[\\mu m]$"
        label_m: "$S_d^{n}$ $[\\mu m]$"
      delta:
        label_d: "$\\Delta_d^{n+1}$ $[\\mu m]$"
        label_m: "$\\Delta_d^{n}$ $[\\mu m]$"
      growth_rate:
        label_d: "$\\lambda^{n+1}$ $[h^{-1}]$"
        label_m: "$\\lambda^{n}$ $[h^{-1}]$"
        scale: 60.
      tau:
        label_d: "$\\tau^{n+1}$ $[min]$"
        label_m: "$\\tau^{n}$ $[min]$"
      taucyc_min:
        label_d: "$\\tau_{cyc}^{n+1}$ $[min]$"
        label_m: "$\\tau_{cyc}^{n}$ $[min]$"
      C_min:
        label_d: "$C^{n+1}$ $[min]$"
        label_m: "$C^{n}$ $[min]$"
      D_min:
        label_d: "$D^{n+1}$ $[min]$"
        label_m: "$D^{n}$ $[min]$"
      unit_size:
        label_d: "$S_{0}^{n+1}$ $[\\mu m]$"
        label_m: "$S_{0}^{n}$ $[\\mu m]$"
    args:
      method: pearsonr
      #method: spearmanr

  plot_lineages_byfov:
  # comment fovs to plot all lineages
  # put fovs key with None value to disable plotting
    fovs:
    args:
      color: black
      ax_height: 3
      ax_width_per_hour: 2

  plot_lineages_with_growth_rate:
  # comment fovs to plot all lineages
  # put fovs key with None value to disable plotting
  #    fovs:
  #      6: [1692]
    args:
      color: black
      stitch: True
      logscale: True
      pfit: 3
      showfits: False

  plot_lineages_variables:
    attributes:
      growth_rate:
        label: "$\\lambda$ $[h^{-1}]$"
        scale: 60.
      delta:
        label: "$\\Delta_d$ $[\\mu m]$"
      sb:
        label: "$S_b$ $[\\mu m]$"
        #    fovs:
        #      6: [1692]
    args:
      color: black
      color1: darkblue
      stitch: False
      logscale: True

  plot_lineages_correlations:
    attributes:
      growth_rate:
        label: "$\\lambda$ $[h^{-1}]$"
        label_d: "$\\lambda^{n+1}$ $[h^{-1}]$"
        label_m: "$\\lambda^{n}$ $[h^{-1}]$"
        scale: 60.
      delta:
        label: "$\\Delta_d$ $[\\mu m]$"
        label_d: "$\\Delta_d^{n+1}$ $[\\mu m]$"
        label_m: "$\\Delta_d^{n}$ $[\\mu m]$"
      sb:
        label: "$S_b$ $[\\mu m]$"
        label_d: "$S_b^{n+1}$ $[\\mu m]$"
        label_m: "$S_b^{n}$ $[\\mu m]$"
      sd:
        label: "$S_d$ $[\\mu m]$"
        label_d: "$S_d^{n+1}$ $[\\mu m]$"
        label_m: "$S_d^{n}$ $[\\mu m]$"
        #    fovs:
        #      6: [1692]
    args:
      color: black
      color1: darkblue
      stitch: False
      logscale: True