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configuration_files.py
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configuration_files.py
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"""
Functions to create and load configuration files required to run the pipeline
"""
from typing import *
import yaml
import sys
import shutil
import pandas as pd
from pathlib import Path
from collections import OrderedDict
from pysmFISH.logger_utils import selected_logger
# to avoid reference for nested structures
# https://stackoverflow.com/questions/13518819/avoid-references-in-pyyaml (comment)
yaml.SafeDumper.ignore_aliases = lambda *args : True
def create_general_analysis_config_file(config_db_path:str):
"""Function to create the basic standard configuration files with all the parameters used for running
all possible analysis. It will be stored in the config_db folder. The data required for a specific analysis
will be extracted from the file according to the information in the experiment_info file.
Args:
config_db_path (str): Path to the config_db folder (ex. ~/XX/XX/config_db)
"""
logger = selected_logger()
config_db_path = Path(config_db_path)
analysis_config_fpath = config_db_path / 'analysis_config.yaml'
analysis_parameters = OrderedDict()
analysis_parameters['eel-barcoded'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH1'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH1']['staining'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH1']['fresh-tissue'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH1']['BarcodesExtractionResolution'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH1']['RegistrationReferenceHybridization'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH1']['RegistrationTollerancePxl'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH1']['RegistrationMinMatchingBeads'] = 5
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['CountingFishMinObjDistance'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['CountingFishMinObjSize'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['CountingFishNumPeaksPerLabel'] = 20
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['LargeObjRemovalPercentile'] = 95
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['ROBOFISH1']['fish']['LargeObjRemovalSelem'] = 7
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['CountingFishMinObjSize'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['ROBOFISH1']['small-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['CountingFishMinObjSize'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['ROBOFISH1']['large-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['CountingFishMinObjDistance'] = 5
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['CountingFishMaxObjSize'] = 600
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['CountingFishMinObjSize'] = 10
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['LargeObjRemovalPercentile'] = 95
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['LargeObjRemovalMinObjSize'] = 100
analysis_parameters['eel-barcoded']['ROBOFISH1']['both-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH1']['staining']['PreprocessingStainingFlatFieldKernel'] = (2,100, 100)
analysis_parameters['eel-barcoded']['ROBOFISH1']['fresh-tissue']['nuclei']= {}
analysis_parameters['eel-barcoded']['ROBOFISH1']['fresh-tissue']['nuclei']['PreprocessingFreshNucleiLargeKernelSize'] = (5,50,50)
analysis_parameters['eel-barcoded']['ROBOFISH1']['fresh-tissue']['beads']= {}
analysis_parameters['eel-barcoded']['ROBOFISH1']['fresh-tissue']['beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['eel-barcoded']['ROBOFISH1']['fresh-tissue']['beads']['CountingFishMinObjDistance'] = 20
analysis_parameters['eel-barcoded']['ROBOFISH1']['fresh-tissue']['beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH1']['fresh-tissue']['beads']['CountingFishMinObjSize'] = 20
analysis_parameters['eel-barcoded']['ROBOFISH1']['fresh-tissue']['beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH2'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH2']['staining'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH2']['fresh-tissue'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH2']['BarcodesExtractionResolution'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH2']['RegistrationReferenceHybridization'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH2']['RegistrationTollerancePxl'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH2']['RegistrationMinMatchingBeads'] = 5
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['CountingFishMinObjDistance'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['CountingFishMinObjSize'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['CountingFishNumPeaksPerLabel'] = 20
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['LargeObjRemovalPercentile'] = 95
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['ROBOFISH2']['fish']['LargeObjRemovalSelem'] = 7
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['CountingFishMinObjSize'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['ROBOFISH2']['small-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['CountingFishMinObjDistance'] = 5
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['CountingFishMaxObjSize'] = 600
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['CountingFishMinObjSize'] = 10
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['ROBOFISH2']['large-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['CountingFishMinObjDistance'] = 5
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['CountingFishMaxObjSize'] = 600
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['CountingFishMinObjSize'] = 10
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['LargeObjRemovalPercentile'] = 95
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['LargeObjRemovalMinObjSize'] = 100
analysis_parameters['eel-barcoded']['ROBOFISH2']['both-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH2']['staining']['PreprocessingStainingFlatFieldKernel'] = (2,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH2']['fresh-tissue']['nuclei']= {}
analysis_parameters['eel-barcoded']['ROBOFISH2']['fresh-tissue']['nuclei']['PreprocessingFreshNucleiLargeKernelSize'] = (5,50,50)
analysis_parameters['eel-barcoded']['ROBOFISH2']['fresh-tissue']['beads']= {}
analysis_parameters['eel-barcoded']['ROBOFISH2']['fresh-tissue']['beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['eel-barcoded']['ROBOFISH2']['fresh-tissue']['beads']['CountingFishMinObjDistance'] = 20
analysis_parameters['eel-barcoded']['ROBOFISH2']['fresh-tissue']['beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH2']['fresh-tissue']['beads']['CountingFishMinObjSize'] = 20
analysis_parameters['eel-barcoded']['ROBOFISH2']['fresh-tissue']['beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH3'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH3']['staining'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH3']['fresh-tissue'] = {}
analysis_parameters['eel-barcoded']['ROBOFISH3']['BarcodesExtractionResolution'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH3']['RegistrationReferenceHybridization'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH3']['RegistrationTollerancePxl'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH3']['RegistrationMinMatchingBeads'] = 5
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['CountingFishMinObjDistance'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['CountingFishMinObjSize'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['CountingFishNumPeaksPerLabel'] = 20
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['LargeObjRemovalPercentile'] = 95
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['ROBOFISH3']['fish']['LargeObjRemovalSelem'] = 7
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['CountingFishMinObjSize'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['LargeObjRemovalPercentile'] = 95
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['ROBOFISH3']['small-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['CountingFishMinObjDistance'] = 5
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['CountingFishMaxObjSize'] = 600
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['CountingFishMinObjSize'] = 10
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['ROBOFISH3']['large-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['CountingFishMinObjDistance'] = 5
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['CountingFishMaxObjSize'] = 600
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['CountingFishMinObjSize'] = 10
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['LargeObjRemovalPercentile'] = 95
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['LargeObjRemovalMinObjSize'] = 100
analysis_parameters['eel-barcoded']['ROBOFISH3']['both-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['ROBOFISH3']['staining']['PreprocessingStainingFlatFieldKernel'] = (2,100,100)
analysis_parameters['eel-barcoded']['ROBOFISH3']['fresh-tissue']['nuclei']= {}
analysis_parameters['eel-barcoded']['ROBOFISH3']['fresh-tissue']['nuclei']['PreprocessingFreshNucleiLargeKernelSize'] = (5,50,50)
analysis_parameters['eel-barcoded']['ROBOFISH3']['fresh-tissue']['beads']= {}
analysis_parameters['eel-barcoded']['ROBOFISH3']['fresh-tissue']['beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['eel-barcoded']['ROBOFISH3']['fresh-tissue']['beads']['CountingFishMinObjDistance'] = 20
analysis_parameters['eel-barcoded']['ROBOFISH3']['fresh-tissue']['beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['ROBOFISH3']['fresh-tissue']['beads']['CountingFishMinObjSize'] = 20
analysis_parameters['eel-barcoded']['ROBOFISH3']['fresh-tissue']['beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['NOT_DEFINED'] = {}
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish'] = {}
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads'] = {}
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads'] = {}
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads'] = {}
analysis_parameters['eel-barcoded']['NOT_DEFINED']['staining'] = {}
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fresh-tissue'] = {}
analysis_parameters['eel-barcoded']['NOT_DEFINED']['BarcodesExtractionResolution'] = 2
analysis_parameters['eel-barcoded']['NOT_DEFINED']['RegistrationReferenceHybridization'] = 1
analysis_parameters['eel-barcoded']['NOT_DEFINED']['RegistrationTollerancePxl'] = 3
analysis_parameters['eel-barcoded']['NOT_DEFINED']['RegistrationMinMatchingBeads'] = 5
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['CountingFishMinObjDistance'] = 2
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['CountingFishMinObjSize'] = 1
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['CountingFishNumPeaksPerLabel'] = 20
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['LargeObjRemovalPercentile'] = 95
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fish']['LargeObjRemovalSelem'] = 7
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['CountingFishMinObjSize'] = 2
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['NOT_DEFINED']['small-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['CountingFishMinObjSize'] = 2
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['eel-barcoded']['NOT_DEFINED']['large-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['CountingFishMinObjDistance'] = 5
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['CountingFishMaxObjSize'] = 600
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['CountingFishMinObjSize'] = 10
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['LargeObjRemovalPercentile'] = 95
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['LargeObjRemovalMinObjSize'] = 100
analysis_parameters['eel-barcoded']['NOT_DEFINED']['both-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['eel-barcoded']['NOT_DEFINED']['staining']['PreprocessingStainingFlatFieldKernel'] = (2,100,100)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fresh-tissue']['nuclei']= {}
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fresh-tissue']['nuclei']['PreprocessingFreshNucleiLargeKernelSize'] = (5,50,50)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fresh-tissue']['beads']= {}
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fresh-tissue']['beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fresh-tissue']['beads']['CountingFishMinObjDistance'] = 20
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fresh-tissue']['beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fresh-tissue']['beads']['CountingFishMinObjSize'] = 20
analysis_parameters['eel-barcoded']['NOT_DEFINED']['fresh-tissue']['beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial'] = {}
analysis_parameters['smfish-serial']['ROBOFISH1'] = {}
analysis_parameters['smfish-serial']['ROBOFISH1']['fish'] = {}
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads'] = {}
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads'] = {}
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads'] = {}
analysis_parameters['smfish-serial']['ROBOFISH1']['staining'] = {}
analysis_parameters['smfish-serial']['ROBOFISH1']['nuclei'] = {}
analysis_parameters['smfish-serial']['ROBOFISH1']['fresh-tissue'] = {}
analysis_parameters['smfish-serial']['ROBOFISH1']['BarcodesExtractionResolution'] = 3
analysis_parameters['smfish-serial']['ROBOFISH1']['RegistrationReferenceHybridization'] = 1
analysis_parameters['smfish-serial']['ROBOFISH1']['RegistrationTollerancePxl'] = 3
analysis_parameters['smfish-serial']['ROBOFISH1']['RegistrationMinMatchingBeads'] = 5
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['CountingFishMinObjDistance'] = 2
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['CountingFishMinObjSize'] = 3
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['CountingFishNumPeaksPerLabel'] = 20
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['LargeObjRemovalPercentile'] = 95
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['smfish-serial']['ROBOFISH1']['fish']['LargeObjRemovalSelem'] = 7
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['CountingFishMinObjSize'] = 2
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['smfish-serial']['ROBOFISH1']['small-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['CountingFishMinObjSize'] = 2
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['smfish-serial']['ROBOFISH1']['large-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.2,0.1,0.1)
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['CountingFishMinObjDistance'] = 5
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['CountingFishMaxObjSize'] = 600
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['CountingFishMinObjSize'] = 10
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['LargeObjRemovalPercentile'] = 95
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['LargeObjRemovalMinObjSize'] = 100
analysis_parameters['smfish-serial']['ROBOFISH1']['both-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['smfish-serial']['ROBOFISH1']['nuclei']['PreprocessingNucleiFlatFieldKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH1']['staining']['PreprocessingStainingFlatFieldKernel'] = (2,100, 100)
analysis_parameters['smfish-serial']['ROBOFISH1']['fresh-tissue']['nuclei']= {}
analysis_parameters['smfish-serial']['ROBOFISH1']['fresh-tissue']['nuclei']['PreprocessingFreshNucleiLargeKernelSize'] = (5,50,50)
analysis_parameters['smfish-serial']['ROBOFISH1']['fresh-tissue']['beads']= {}
analysis_parameters['smfish-serial']['ROBOFISH1']['fresh-tissue']['beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['smfish-serial']['ROBOFISH1']['fresh-tissue']['beads']['CountingFishMinObjDistance'] = 20
analysis_parameters['smfish-serial']['ROBOFISH1']['fresh-tissue']['beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH1']['fresh-tissue']['beads']['CountingFishMinObjSize'] = 20
analysis_parameters['smfish-serial']['ROBOFISH1']['fresh-tissue']['beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH2'] = {}
analysis_parameters['smfish-serial']['ROBOFISH2']['fish'] = {}
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads'] = {}
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads'] = {}
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads'] = {}
analysis_parameters['smfish-serial']['ROBOFISH2']['staining'] = {}
analysis_parameters['smfish-serial']['ROBOFISH2']['nuclei'] = {}
analysis_parameters['smfish-serial']['ROBOFISH2']['fresh-tissue'] = {}
analysis_parameters['smfish-serial']['ROBOFISH2']['BarcodesExtractionResolution'] = 3
analysis_parameters['smfish-serial']['ROBOFISH2']['RegistrationReferenceHybridization'] = 1
analysis_parameters['smfish-serial']['ROBOFISH2']['RegistrationTollerancePxl'] = 3
analysis_parameters['smfish-serial']['ROBOFISH2']['RegistrationMinMatchingBeads'] = 5
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['CountingFishMinObjDistance'] = 1
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['CountingFishMinObjSize'] = 1
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['CountingFishNumPeaksPerLabel'] = 20
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['LargeObjRemovalPercentile'] = 95
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['smfish-serial']['ROBOFISH2']['fish']['LargeObjRemovalSelem'] = 7
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['CountingFishMinObjDistance'] = 1
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['CountingFishMaxObjSize'] = 5
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['CountingFishMinObjSize'] = 1
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['smfish-serial']['ROBOFISH2']['small-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['CountingFishMinObjSize'] = 2
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['smfish-serial']['ROBOFISH2']['large-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['CountingFishMinObjDistance'] = 5
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['CountingFishMaxObjSize'] = 600
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['CountingFishMinObjSize'] = 10
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['LargeObjRemovalPercentile'] = 95
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['LargeObjRemovalMinObjSize'] = 100
analysis_parameters['smfish-serial']['ROBOFISH2']['both-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['smfish-serial']['ROBOFISH2']['nuclei']['PreprocessingNucleiFlatFieldKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH2']['staining']['PreprocessingStainingFlatFieldKernel'] = (2,100, 100)
analysis_parameters['smfish-serial']['ROBOFISH2']['fresh-tissue']['nuclei']= {}
analysis_parameters['smfish-serial']['ROBOFISH2']['fresh-tissue']['nuclei']['PreprocessingFreshNucleiLargeKernelSize'] = (5,50,50)
analysis_parameters['smfish-serial']['ROBOFISH2']['fresh-tissue']['beads']= {}
analysis_parameters['smfish-serial']['ROBOFISH2']['fresh-tissue']['beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['smfish-serial']['ROBOFISH2']['fresh-tissue']['beads']['CountingFishMinObjDistance'] = 20
analysis_parameters['smfish-serial']['ROBOFISH2']['fresh-tissue']['beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH2']['fresh-tissue']['beads']['CountingFishMinObjSize'] = 20
analysis_parameters['smfish-serial']['ROBOFISH2']['fresh-tissue']['beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH3'] = {}
analysis_parameters['smfish-serial']['ROBOFISH3']['fish'] = {}
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads'] = {}
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads'] = {}
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads'] = {}
analysis_parameters['smfish-serial']['ROBOFISH3']['staining'] = {}
analysis_parameters['smfish-serial']['ROBOFISH3']['nuclei'] = {}
analysis_parameters['smfish-serial']['ROBOFISH3']['fresh-tissue'] = {}
analysis_parameters['smfish-serial']['ROBOFISH3']['BarcodesExtractionResolution'] = 3
analysis_parameters['smfish-serial']['ROBOFISH3']['RegistrationReferenceHybridization'] = 1
analysis_parameters['smfish-serial']['ROBOFISH3']['RegistrationTollerancePxl'] = 3
analysis_parameters['smfish-serial']['ROBOFISH3']['RegistrationMinMatchingBeads'] = 5
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['CountingFishMinObjDistance'] = 1
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['CountingFishMinObjSize'] = 1
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['CountingFishNumPeaksPerLabel'] = 20
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['LargeObjRemovalPercentile'] = 95
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['smfish-serial']['ROBOFISH3']['fish']['LargeObjRemovalSelem'] = 7
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['PreprocessingFishFlatFieldKernel'] = (3,100,100)
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['CountingFishMaxObjSize'] = 5
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['CountingFishMinObjSize'] = 1
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['smfish-serial']['ROBOFISH3']['small-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['CountingFishMinObjDistance'] = 2
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['CountingFishMinObjSize'] = 2
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['LargeObjRemovalPercentile'] = 99
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['LargeObjRemovalMinObjSize'] = 50
analysis_parameters['smfish-serial']['ROBOFISH3']['large-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['PreprocessingFishFilteringSmallKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['PreprocessingFishFilteringLaplacianKernel'] = (0.02,0.01,0.01)
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['PreprocessingFishFlatFieldKernel'] = (1,100,100)
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['CountingFishMinObjDistance'] = 5
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['CountingFishMaxObjSize'] = 600
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['CountingFishMinObjSize'] = 10
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['CountingFishNumPeaksPerLabel'] = 1
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['LargeObjRemovalPercentile'] = 95
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['LargeObjRemovalMinObjSize'] = 100
analysis_parameters['smfish-serial']['ROBOFISH3']['both-beads']['LargeObjRemovalSelem'] = 3
analysis_parameters['smfish-serial']['ROBOFISH3']['nuclei']['PreprocessingNucleiFlatFieldKernel'] = (1,8,8)
analysis_parameters['smfish-serial']['ROBOFISH3']['staining']['PreprocessingStainingFlatFieldKernel'] = (2,100, 100)
analysis_parameters['smfish-serial']['ROBOFISH3']['fresh-tissue']['nuclei']= {}
analysis_parameters['smfish-serial']['ROBOFISH3']['fresh-tissue']['nuclei']['PreprocessingFreshNucleiLargeKernelSize'] = (5,50,50)
analysis_parameters['smfish-serial']['ROBOFISH3']['fresh-tissue']['beads']= {}
analysis_parameters['smfish-serial']['ROBOFISH3']['fresh-tissue']['beads']['PreprocessingFishFlatFieldKernel'] = (100,100)
analysis_parameters['smfish-serial']['ROBOFISH3']['fresh-tissue']['beads']['CountingFishMinObjDistance'] = 20
analysis_parameters['smfish-serial']['ROBOFISH3']['fresh-tissue']['beads']['CountingFishMaxObjSize'] = 200
analysis_parameters['smfish-serial']['ROBOFISH3']['fresh-tissue']['beads']['CountingFishMinObjSize'] = 20
analysis_parameters['smfish-serial']['ROBOFISH3']['fresh-tissue']['beads']['CountingFishNumPeaksPerLabel'] = 1
try:
with open(analysis_config_fpath, 'w') as new_config:
yaml.safe_dump(dict(analysis_parameters), new_config,default_flow_style=False,sort_keys=False)
except:
logger.error(f'cannot save the analysis_config_file')
def create_function_runner(experiment_fpath: str,metadata: dict)-> dict:
"""Function used to define which preprocessing and counting functions will
be run in a pipeline. This allows to run multiple pipeline using the same
code. The name of the pipeline selected is stored in the metadata and extracted
from the experiment configuration file
Args:
experiment_fpath (str): Path to the folder with the experiments to process.
metadata (dict): Metadata related to the experiment to process
Returns:
dict: Running function (name:function name)
"""
logger = selected_logger()
experiment_fpath = Path(experiment_fpath)
running_functions = OrderedDict()
pipeline = metadata['pipeline']
stitching_type = metadata['stitching_type']
if pipeline == 'eel-human-GBM':
running_functions = { 'fish_channels_preprocessing':'filter_remove_large_objs',
'fish_channels_dots_calling':'osmFISH_peak_based_detection_fast',
'fresh_sample_reference_preprocessing':'fresh_tissue_beads_preprocessing',
'fresh_sample_reference_dots_calling':'osmFISH_peak_based_detection_fast',
'fresh_sample_nuclei_preprocessing':'fresh_nuclei_filtering'}
logger.info(f'selected functions for {pipeline}')
elif pipeline == 'eel-human-adult-brain':
running_functions = { 'fish_channels_preprocessing':'filter_remove_large_objs',
'fish_channels_dots_calling':'osmFISH_peak_based_detection_fast',
'fresh_sample_reference_preprocessing':'fresh_tissue_beads_preprocessing',
'fresh_sample_reference_dots_calling':'osmFISH_peak_based_detection_fast',
'fresh_sample_nuclei_preprocessing':'fresh_nuclei_filtering'}
logger.info(f'selected functions for {pipeline}')
elif pipeline == 'eel-human-embryo':
running_functions = { 'fish_channels_preprocessing':'standard_not_norm_preprocessing',
'fish_channels_dots_calling':'osmFISH_peak_based_detection_fast',
'fresh_sample_reference_preprocessing':'fresh_tissue_beads_preprocessing',
'fresh_sample_reference_dots_calling':'osmFISH_peak_based_detection_fast',
'fresh_sample_nuclei_preprocessing':'fresh_nuclei_filtering'}
elif pipeline == 'eel-mouse-brain':
running_functions = { 'fish_channels_preprocessing':'standard_not_norm_preprocessing',
'fish_channels_dots_calling':'osmFISH_peak_based_detection_fast',
'fresh_sample_reference_preprocessing':'fresh_tissue_beads_preprocessing',
'fresh_sample_reference_dots_calling':'osmFISH_peak_based_detection_fast',
'fresh_sample_nuclei_preprocessing':'fresh_nuclei_filtering'}
elif pipeline == 'smfish-serial-adult-human':
running_functions = { 'fish_channels_preprocessing':'filter_remove_large_objs',
'fish_channels_dots_calling':'osmFISH_peak_based_detection_fast',
'reference_channels_preprocessing':'nuclei_registration_filtering',
'registration_reference':'calculate_shift_hybridization_fov_nuclei',
'registration_fish': 'register_fish_on_nuclei'}
elif pipeline == 'smfish-serial-mouse':
running_functions = { 'fish_channels_preprocessing':'standard_not_norm_preprocessing',
'fish_channels_dots_calling':'osmFISH_peak_based_detection_fast'}
elif pipeline == 'smFISH-serial':
running_functions = { 'fish_channels_preprocessing':'standard_not_norm_preprocessing',
'fish_channels_dots_calling':'osmFISH_peak_based_detection_fast'}
elif pipeline == 'smfish-serial-controls-eel':
running_functions = { 'fish_channels_preprocessing':'standard_not_norm_preprocessing',
'fish_channels_dots_calling':'osmFISH_peak_based_detection_fast'}
logger.info(f'selected functions for {pipeline}')
else:
logger.error(f'The sample does not have a corresponding analysis pipeline')
sys.exit(f'The sample does not have a corresponding analysis pipeline')
if stitching_type == 'large-beads':
running_functions['reference_channels_preprocessing'] = 'large_beads_preprocessing'
running_functions['reference_channels_dots_calling'] = 'beads_peak_based_detection'
elif stitching_type == 'small-beads':
running_functions['reference_channels_preprocessing'] = 'standard_not_norm_preprocessing'
running_functions['reference_channels_dots_calling'] = 'beads_peak_based_detection'
elif stitching_type == 'both-beads':
running_functions['reference_channels_preprocessing'] = 'both_beads_preprocessing'
running_functions['reference_channels_dots_calling'] = 'beads_peak_based_detection'
elif stitching_type == 'nuclei':
running_functions['reference_channels_preprocessing'] = 'nuclei_registration_filtering'
try:
analysis_config_fpath = experiment_fpath / 'pipeline_config' / 'running_functions.yaml'
with open(analysis_config_fpath, 'w') as new_config:
yaml.safe_dump(dict(running_functions), new_config,default_flow_style=False,sort_keys=False)
except:
logger.error(f'cannot save the analysis_config_file')
return running_functions
def create_specific_analysis_config_file(experiment_fpath:str, experiment_info:Dict):
"""Select the analysis parameters from the general analysis_config.yaml according
to the processing machine. If the machine is not defined in the experiment_info
dictionary a generic processing set up is defined
Args:
experiment_fpath (str): Path to the experiment to process
experiment_info (Dict): Experiment configuration info
"""
logger = selected_logger()
experiment_fpath = Path(experiment_fpath)
general_analysis_config_fpath = experiment_fpath.parent / 'config_db' / 'analysis_config.yaml'
analysis_config_fpath = experiment_fpath / 'pipeline_config' / 'analysis_config.yaml'
analysis_config = OrderedDict()
general_analysis_config = yaml.safe_load(open(general_analysis_config_fpath, 'rb'))
try:
yaml.safe_load(open(analysis_config_fpath,'rb'))
logger.debug(f'The analysis config file is already present')
except:
try:
machine = experiment_info['Machine']
except NameError:
machine = 'NOT_DEFINED'
try:
experiment_type = experiment_info['Experiment_type']
analysis_config = general_analysis_config[experiment_type][machine]
beads_keys = [el for el in analysis_config.keys() if 'beads' in el]
selected_stitching = experiment_info['Stitching_type']
if 'beads' in selected_stitching:
beads_keys.remove(selected_stitching)
for el in beads_keys:
analysis_config.pop(el, None)
analysis_config.pop('nuclei', None)
elif selected_stitching == 'nuclei':
for el in beads_keys:
analysis_config.pop(el, None)
except:
logger.error(f'Unidentified experiment type in the config.yaml file')
else:
try:
with open(analysis_config_fpath, 'w') as new_config:
yaml.safe_dump(dict(analysis_config), new_config,default_flow_style=False,sort_keys=False)
except:
logger.error(f'cannot save the analysis_config_file')
"""
Select the analysis parameters according to the processing machine. If the
machine is not defined in the experiment_info dictionary a generic processing set up is defined
Args:
experiment_fpath: str
path to the experiment that will be processed
experiment_info: dict
dictionary containing all the info generated by robofish
"""
def create_analysis_config_file_from_dataset(experiment_fpath: str, metadata: dict):
"""Select the analysis parameters according to the processing machine. If the
machine is not defined in the experiment_info dictionary a generic processing set up is defined.
IMPORTANT: If the analysis_config.yaml file is already present in the
pipeline_config folder it does not overwrite it.
Args:
experiment_fpath (str): Path to the experiment to process
metadata (dict): Metadata related to the experiment to process
Returns:
dict: analysis_config parameters
"""
logger = selected_logger()
general_analysis_config_fpath = experiment_fpath.parent / 'config_db' / 'analysis_config.yaml'
analysis_config = OrderedDict()
analysis_config_fpath = experiment_fpath / 'pipeline_config' / 'analysis_config.yaml'
try:
analysis_config = yaml.safe_load(open(analysis_config_fpath,'rb'))
logger.debug(f'The analysis config file is already present')
return dict(analysis_config)
except:
try:
machine = metadata['machine']
except NameError:
machine = 'NOT_DEFINED'
try:
general_analysis_config = yaml.safe_load(open(general_analysis_config_fpath, 'rb'))
experiment_type = metadata['experiment_type']
analysis_config = general_analysis_config[experiment_type][machine]
beads_keys = [el for el in analysis_config.keys() if 'beads' in el]
selected_stitching = metadata['stitching_type']
if 'beads' in selected_stitching:
beads_keys.remove(selected_stitching)
for el in beads_keys:
analysis_config.pop(el, None)
analysis_config.pop('nuclei', None)
elif selected_stitching == 'nuclei':
for el in beads_keys:
analysis_config.pop(el, None)
except:
logger.error(f'Unidentified experiment type {experiment_type}')
else:
try:
with open(analysis_config_fpath, 'w') as new_config:
yaml.safe_dump(dict(analysis_config), new_config,default_flow_style=False,sort_keys=False)
return dict(analysis_config)
except:
logger.error(f'cannot save the analysis_config_file')
def load_experiment_config_file(experiment_fpath:str):
"""Function that load the experiment configuration file
Args:
experiment_fpath (str): Path to the experiment to process
Returns:
dict: Experiment configuration parameters
"""
logger = selected_logger()
experiment_fpath = Path(experiment_fpath)
experiment_name = experiment_fpath.stem
experiment_name = experiment_name.split('_auto')[0]
search_key = experiment_name + '_config.yaml'
try:
experiment_info_fpath = list(experiment_fpath.glob(search_key))[0]
except:
logger.error(f'No experiment info file in {experiment_fpath}')
sys.exit(f'No experiment info file in {experiment_fpath}')
else:
try:
experiment_info = yaml.safe_load(open(experiment_info_fpath, 'rb'))
return experiment_info
except:
logger.error(f'Experiment info file has the wrong name in {experiment_fpath}')
sys.exit(f'Experiment info file has the wrong name in {experiment_fpath}')
def load_codebook(experiment_fpath:str, metadata:str)-> dict:
"""Function used to load the codebooks. It links the channel to
the codebook pandas dataframe
Args:
experiment_fpath (str): Path to the experiment to process
metadata (dict): Metadata related to the experiment to process
Returns:
dict: Dictionary with all codebooks required for processing
"""
logger = selected_logger()
all_codebooks_dict = {}
for channel, codebook_name in zip(metadata['list_all_channels'],metadata['list_all_codebooks']):
if codebook_name != 'None':
codebook_fpath = Path(experiment_fpath) / 'codebook' / codebook_name
try:
codebook = pd.read_parquet(codebook_fpath)
except (FileExistsError,NameError,FileNotFoundError) as e:
logger.debug(f'{codebook_name} missing in the pipeline_config folder')
try:
codebooks_db_fpath = (Path(experiment_fpath)).parent / 'codebooks' / codebook_name
codebook = pd.read_parquet(codebooks_db_fpath)
_ = shutil.copy2(codebooks_db_fpath,codebook_fpath)
all_codebooks_dict[channel] = codebook
except:
logger.error(f'cannot create the codebook')
sys.exit(f'cannot create the codebook')
else:
all_codebooks_dict[channel] = codebook
return all_codebooks_dict
def load_analysis_config_file(experiment_fpath:str)-> dict:
"""Load the analysis configuration file used for the processing
stored in the pipeline_config folder
Args:
experiment_fpath (str): Path to the experiment to process
Returns:
dict: Analysis configuration parameters
"""
logger = selected_logger()
experiment_fpath = Path(experiment_fpath)
analysis_config_fpath = experiment_fpath / 'pipeline_config' / 'analysis_config.yaml'
try:
analysis_config = OrderedDict(yaml.safe_load(open(analysis_config_fpath, 'rb')))
except (FileExistsError,NameError,FileNotFoundError) as e:
logger.debug(f'{analysis_config_fpath} missing')
else:
return analysis_config