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old_analysis_settings.py
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experiments = {
'Test': {
# name: folder 0
'name': 'Test',
# root: path to folder
'root': 'C:\\Users\\fjs21\\OneDrive\\Research&Lab\\Data\\Transwell Experiments 2020',
# pattern: define file
'pattern': '*.tif',
# which channel is DAPI?
'dapi_ch': 0,
# which channel is O4?
'o4_ch': None,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
},
'Roopa September 2020 BK experiment': {
# name: folder 1
'name': 'Roopa September 2020 BK experiment',
# root: path to folder
'root': 'C:\\scratch\\sep 2020 sample',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 1,
# which channel is O4?
'o4_ch': 2,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set gamma and treshold method
'gamma': 0.5,
'thres': 'th2', },
'Jackie Transwell and IGFBP2 experiment': {
# name: folder 2
'name': 'Jackie Transwell and IGFBP2 experiment',
# root: path to folder
'root': 'C:\\scratch\\Transwell + IGFBP2 Ab',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
# which channel is O4?
'o4_ch': None,
# which channel is EdU?
'EdU_ch': 1,
# which marker counts the O4 counts
'marker_index': None,
# set gamma and treshold method
'gamma': 1.0,
'thres': 'th2', },
'Roopa Feb 2020 BK experiment': {
# name: folder 3
'name': 'Roopa Feb 2020 BK experiment',
# root: path to folder
'root': 'Y:\\People\\Roopa\\dk si alpha expts\\feb 2020 sample',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 1,
# which channel is O4?
'o4_ch': 2,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set gamma and treshold method
'gamma': 0.5,
'thres': 'th2', },
'Roopa July 2020 BK experiment (Discard)': {
# name: folder 4
'name': 'Roopa July 2020 BK experiment (Discard)',
# root: path to folder
'root': 'Y:\\People\\Roopa\\dk si alpha expts\\july 2020',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 1,
# which channel is O4?
'o4_ch': 2,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set gamma
'gamma': 0.5,
'thres': 'th2',
},
"Ahmed's transwell experiment": {
# name: folder 5
'name': "Ahmed's transwell experiment",
# root: path to folder
'root': 'Y:\\People\\Ahmed\\Transwell Experiments\\Exp 3\\Proliferation',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
# which channel is O4?
'o4_ch': None,
# which channel is EdU?
'EdU_ch': 1,
# which marker counts the O4 counts
'marker_index': None,
# set gamma
'gamma': 3.5,
'thres': 'th2',
},
"Roopa July 31 2019 BK experiment": {
# name: folder 6
'name': "Roopa July 31 2019 BK experiment",
# root: path to folder
'root': 'Y:\\People\\Roopa\\dk si alpha expts\\siBK 0731 sample',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 1,
'dapi_gamma': 0.5,
# which channel is O4?
'o4_ch': 2,
'o4_gamma': 0.2,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set threshold
'thres': 'th2',
},
"Test of DAPI/GFP transwell images": {
# name: folder 7
'name': "Test of DAPI/GFP transwell images",
# root: path to folder
# 'root': 'C:\\scratch\\Migration Assays',
'root': 'C:\\Users\fjs21\\Box\\NewLabData\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(1) no A594',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
# which channel is O4?
'o4_ch': None,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set gamma
'gamma': 1,
'thres': 'th2',
},
"Migration Assay (Experiment 1) - DAPI/GFP/A594 transwell images": {
# name: folder 8
'name': "Migration Assay (Experiment 1) - DAPI/GFP/A594 transwell images",
# root: path to folder
# 'root': 'Y:\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(1)',
'root': 'C:\\Users\\fjs21\\Box\\NewLabData\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(1)',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 1.0,
# which channel is O4?
'o4_ch': None,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
},
"Migration Assay (Experiment 2) - DAPI/GFP/A594 transwell images": {
# name: folder 9
'name': "Migration Assay (Experiment 2) - DAPI/GFP/A594 transwell images",
# root: path to folder
# 'root': 'Y:\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(2)',
'root': 'C:\\Users\\fjs21\\Box\\NewLabData\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(2)',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 1.0,
# which channel is O4?
'o4_ch': None,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
},
"Migration Assay (Experiment 3) - DAPI/GFP/A594 transwell images": {
# name: folder 10
'name': "Migration Assay (Experiment 3) - DAPI/GFP/A594 transwell images",
# root: path to folder
'root': 'C:\\Users\\fjs21\\Box\\NewLabData\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(3)',
# 'root': 'Y:\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(3)',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 1.0,
# which channel is O4?
'o4_ch': None,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
},
"Migration Assay (Experiment 4) - DAPI/GFP/A594 transwell images": {
# name: folder 11
'name': "Migration Assay (Experiment 4) - DAPI/GFP/A594 transwell images",
# root: path to folder
# 'root': 'Y:\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(4)',
'root': 'C:\\Users\\fjs21\\Box\\NewLabData\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(4)',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 1.0,
# which channel is O4?
'o4_ch': None,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
},
"Migration Assay (Experiment 5) - DAPI/GFP/A594 transwell images": {
# name: folder 12
'name': "Migration Assay (Experiment 5) - DAPI/GFP/A594 transwell images",
# root: path to folder
'root': 'C:\\Users\\fjs21\\Box\\NewLabData\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(5)',
# 'root': 'Y:\\People\\Jackie\\Migration Assays (SULF2 paper)\\Migration Assay(5)',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 1.0,
# which channel is O4?
'o4_ch': None,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': None,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
},
"Transwell experiment Jan 2021": {
# name: folder 13
'name': "Transwell experiment Jan 2021",
# root: path to folder
'root': 'C:\\Users\\fjs21\\Box\\NewLabData\\People\\Jackie\\Transwell Exps_2021\\Expt 1',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 1.0,
# which channel is O4?
'o4_ch': None,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': 1,
'EdU_gamma': 1.0,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
},
"Transwell experiment Feb 2021": {
# name: folder 14
'name': "Transwell experiment Feb 2021",
# root: path to folder
'root': 'C:\\Users\\fjs21\\Box\\NewLabData\\People\\Jackie\\Transwell Exps_2021\\Expt 2',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 1.0,
# which channel is O4?
'o4_ch': None,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': 1,
'EdU_gamma': 1.0,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
},
"IGFBP2 antibody experiment (Feb 2021)": {
# name: folder 15
'name': "IGFBP2 antibody experiment",
# root: path to folder
'root': 'C:\\Users\\fjs21\\Box\\NewLabData\\People\\Jackie\\IGFBP2\\Feb 2021',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 0.8,
# which channel is O4?
'o4_ch': None,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': 1,
'EdU_gamma': 1.0,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
},
"IGFBP2 antibody experiment (Mar 2021)": {
# name: folder 16
'name': "IGFBP2 antibody experiment",
# root: path to folder
'root': 'C:\\Users\\fjs21\\Box\\NewLabData\\People\\Jackie\\IGFBP2\\Mar 2021',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 0.8,
# which channel is O4?
'o4_ch': None,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': 1,
'EdU_gamma': 1.0,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
},
"Evan's Noggin and OKN experiment": {
# name: folder 17
'name': "Evan's Noggin and OKN experiment",
# root: path to folder
'root': '~/Library/Mobile\ Documents/com~apple~CloudDocs/Research\&Lab/Data/Automated\ Cell\ Counts/2022-03-04\ \(Evans\ OKN\ \&\ Noggin\ plate\)',
# pattern: define file
'pattern': '*.vsi',
# which channel is DAPI?
'dapi_ch': 0,
'dapi_gamma': 0.8,
# which channel is O4?
'o4_ch': 1,
'o4_gamma': 1,
# which channel is EdU?
'EdU_ch': None,
'EdU_gamma': 1.0,
# which marker counts the O4 counts
'marker_index': None,
# set threshold method
'thres': 'th2',
# settings for autoFL channel
'autoFL_dilate': False,
'autoFL_gamma': 1,
}
}
import json
filename = "experiments.json"
with open(filename, "w") as f:
json.dump(experiments, f)