FISH_System_datafile_template.yaml

# Automatic ROBOFISH info
# Make sure to always put a space between the colon and the value!
FISHSystem:
    Parameters:
        #   Operator running the experiment. Same as name linked to Pushbulet code, lower case
        Operator: 
        #   Machine the experiment is run on: ROBOFISH1, ROBOFISH2 or NOT-DEFINED
        Machine: ROBOFISH
        ########## EXPERIMENT 1 ##########
        #   Experiment name: Initials with date, like: LBEXP20181220_1
        EXP_name_1: 
        #   Short description of the Experiment
        Description_1:
        #   Link to the protocol file on Protocols.io
        Protocols_io_1:
        #   YYYYMMDD
        Start_date_1:
        #   Chamber1 or Chamber2
        Chamber_EXP_1: Chamber1
        #   First Hybridization time in hours (encoding probes)
        Hyb_time_1_A: 
        #   Second Hybridization time in hours (amplifier probes)
        Hyb_time_1_B:
        #   Third Hybridization time in hours (detection probes)
        Hyb_time_1_C:
        #   Experiment_type: smfish-serial, smfish-barcoded, eel-barcoded
        Experiment_type_1: 
        #   Total number of rounds
        Target_cycles_1: 
        #   True or False if a barcode is used
        Barcode_1: true
        #   Name of the detection chemisty, like: EELV2_core, EELV2_all, indirect_64
        Chemistry_1: 
        #   Name of the codebooks
        Codebook_DAPI_1:
        Codebook_Atto425_1:
        Codebook_FITC_1:
        Codebook_Cy3_1:
        Codebook_TxRed_1:
        Codebook_Cy5_1: 
        Codebook_Cy7_1:
        Codebook_Europium_1:
        #   True if there are multicolor barcodes
        Multicolor_barcode_1: false
        #   Name of the FASTA file with the probe sequences
        Probes_FASTA_DAPI_1:
        Probes_FASTA_Atto425_1:
        Probes_FASTA_FITC_1:
        Probes_FASTA_Cy3_1:
        Probes_FASTA_TxRed_1:
        Probes_FASTA_Cy5_1:
        Probes_FASTA_Cy7_1:
        Probes_FASTA_Europium_1:
        #   Number of bits in the barcode
        Barcode_length_1: 16
        #   Species:
        Species_1: 
        #   Strain of the animal
        Strain_1:
        #   Sample identification number
        Sample_1:
        #   Age of sample. Use letter indication for age system. Like: e for embryonic or ga for gestational age
        Age_1:
        #   Tissue
        Tissue_1:
        #   Section orientation
        Orientation_1:
        #   Region imaged
        RegionImaged_1:
        #   Section ID
        SectionID_1:
        #   Coordinates of the section. (use appropriate coordinate system for species)
        Position_1:
        #   Stiching type: small-beads, large-beads, both-beads, nuclei
        Stitching_type_1: 
        #   Channel to be used for stitching
        StitchingChannel_1: 
        #   Overlap percentage between fields of view
        Overlapping_percentage_1: 
        #   List of lists with coordinates of the roi's, like: [[0, 120], [121, 237]]
        roi_1: [[0, 0]]
        #   Name of analysis pipeline to use. Options: eel-human-GBM, eel-human-adult-brain, eel-human-embryo
        Pipeline_1:
        ########## EXPERIMENT 2 ##########
        #   Experiment name: Initials with date, like: LBEXP20181220_Mouse_2
        EXP_name_2:
        #   Short description of the Experiment
        Description_2:
        #   Link to the protocol file on Protocols.io
        Protocols_io_2:
        #   YYYY-MM-DD HH:MM
        Start_date_2:
        #   Chamber1 or Chamber2
        Chamber_EXP_2:
        #   First Hybridization time in hours (encoding probes)
        Hyb_time_2_A:
        #   Second Hybridization time in hours (amplifier probes)
        Hyb_time_2_B:
        #   Third Hybridization time in hours (detection probes)
        Hyb_time_2_C:
        #   Experiment_type: smfish-serial, smfish-barcoded
        Experiment_type_2:
        #   Total number of rounds
        Target_cycles_2:
        #   True or False if a barcode is used
        Barcode_2:
        #   Name of the detection chemisty, like:
        Chemistry_2:
        #   Name of the codebooks
        Codebook_DAPI_2:
        Codebook_Atto425_2:
        Codebook_FITC_2:
        Codebook_Cy3_2:
        Codebook_TxRed_2:
        Codebook_Cy5_2:
        Codebook_Cy7_2:
        Codebook_Europium_2:
        #   True if there are multicolor barcodes
        Multicolor_barcode_2: false
        #   Name of the FASTA file with the probe sequences
        Probes_FASTA_DAPI_2:
        Probes_FASTA_Atto425_2:
        Probes_FASTA_FITC_2:
        Probes_FASTA_Cy3_2:
        Probes_FASTA_TxRed_2:
        Probes_FASTA_Cy5_2:
        Probes_FASTA_Cy7_2:
        Probes_FASTA_Europium_2:
        #   Number of bits in the barcode
        Barcode_length_2:
        #   Species:
        Species_2:
        #   Strain of the animal
        Strain_2:
        #   Sample identification number
        Sample_2:
        #   Age of sample. Use letter indication for age system. Like: e for embryonic or ga for gestational age
        Age_2:
        #   Tissue
        Tissue_2:
        #   Section orientation
        Orientation_2:
        #   Region imaged
        RegionImaged_2:
        #   Section ID
        SectionID_2:
        #   Coordinates of the section. (use appropriate coordinate system for species)
        Position_2:
         #   Stiching type: small-beads, large-beads, nuclei
        Stitching_type_2:
        #   Channel to be used for stitching
        StitchingChannel_2:
        #   Overlap percentage between fields of view
        Overlapping_percentage_2:
        #   List of lists with coordinates of the roi's, like: [[1, 120], [121, 237]]
        roi_2: [[0, 0]]
        #   Name of analysis pipeline to use.
        Pipeline_2:
        ########## OTHER ##########
        #   Name of executing protocol for documentation
        Program:
        #   Volume of hybmix in ul
        Hybmix_volume: 500
        #   Temperature used for staining and washing
        Staining_temperature: 37
        #   Temperature used for the readout probes
        Readout_temperature: 22
        #   temperature used for the stripping
        Stripping_temperature: 22
        #   Temperature used for heatshock
        Heatshock_temperature: 22
        #   Temperature used for imaging
        Imaging_temperature: 20
    # Volume of all buffers in ul, Integer/float
    Volumes:
        RunningBuffer: 
        # Port 1-10 on acuator valve 1
        P1: 
        P2: 
        P3: 
        P4: 
        P5: 
        P6: 
        P7: 
        P8: 
        P9: 
        P10: 
        # Port 1-10 on acuator valve 2 are numberd 11-20.
        P11: 
        P12: 
        P13: 
        P14: 
        P15: 
        P16: 
        P17: 
        P18: 
        P19: 
        P20: 
    # Name of the buffer connected to the ports.
    # Use "Waste" for the connection to the waste, "Valve2" for the connection to Valve 2
    # and use HYBXX for the hybridization mixes where XX are a number, like HYB05 or HYB10.
    Ports:
        # Buffer connected to the Syringe pump
        RunningBuffer: 
        # Port 1-10 on acuator valve 1
        P1: 
        P2: 
        P3: 
        P4: 
        P5: 
        P6: 
        P7: 
        P8: 
        P9: 
        P10: 
        # Port 1-10 on acuator valve 2 are numberd 11-20
        P11: 
        P12: 
        P13: 
        P14: 
        P15: 
        P16: 
        P17: 
        P18: 
        P19: 
        P20: 
    # To which Hybridization in which chamber does the HYB X port belong
    # Use "C1" for Chamber1 and "C2" for Chamber2, then append a lower dash plus cycle number
    # Like: "C1_01" for Chamber1 cycle 1 or "C2_14" for Chamber2 cycle 14
    # Append an A or B if you want to use indirect labeling. A for encoding probes, B for detection probes.
    # For indirect labeling use: "C1_01_A" for Chamber 1 cycle 1 hybridization 1 (encoding probes), 
    # "C2_14_B" for Chamber 2, cycle 14, hybridization 2 (detection probes)
    Hybmix:
        # Port 1-10 on acuator valve 1
        P1: 
        P2: 
        P3: 
        P4:
        P5:
        P6:
        P7:
        P8: 
        P9:
        P10:
        # Port 1-10 on acuator valve 2 are numberd 11-20.
        P11:
        P12:
        P13:
        P14:
        P15:
        P16:
        P17:
        P18:
        P19:
        P20:
    # Targets of each round
    # Gene name, Background, polyA, Beads or Nuclei
    Targets:
        ##########    Chamber 1     ##########
        Chamber1:
            Hybridization01:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization02:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization03:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization04:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization05:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization06:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization07:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization08:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization09:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization10:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization11:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization12:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization13:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization14:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization15:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization16:
                DAPI:
                Atto425:
                FITC:
                Cy3: 
                TxRed:
                Cy5: 
                Cy7:
                QDot:
                BrightField:
                Europium: 
            Hybridization17:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization18:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization19:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization20:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization21:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization22:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization23:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization24:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization25:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization26:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization27:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization28:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization29:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization30:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
        ##########    Chamber 2     ##########
        Chamber2:
            Hybridization01:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization02:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization03:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization04:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization05:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization06:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization07:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization08:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization09:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization10:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization11:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization12:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization13:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization14:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization15:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization16:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization17:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization18:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization19:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization20:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization21:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization22:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization23:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization24:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization25:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization26:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization27:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization28:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization29:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
            Hybridization30:
                DAPI:
                Atto425:
                FITC:
                Cy3:
                TxRed:
                Cy5:
                Cy7:
                QDot:
                BrightField:
                Europium:
     # Table with active/connected Machines. Set to 1 for all used machines.
     #If you switch off a machine set the value below to zero. Then the machine will not be checked for errors anymore.
    Machines:
        CavroXE1000: 0
        CavroXCalibur: 1
        MXValve1: 1
        MXValve2: 1
        Degassi: None
        ThermoCube1: 0
        ThermoCube2: 0
        Oasis1: 0
        Oasis2: 0
        YoctoThermistor: 0
        TC720: 1
    #Put the identifiers of each machine here. This will be used to find the USB port for each device.
    #Find the ports using the "find_address()" Function, then paste the device serial number here.
    #This is the safest method.
    Machine_identification:
        CavroXE1000: #not needed
        CavroXCalibur: #not needed
        MXValve1: 
        MXValve2: 
        ThermoCube1:
        ThermoCube2:
        Oasis1:
        Oasis2:
        YoctoThermistor:
        TC720: 
    #If the identifier can not be found, you can use a fixed USB port.
    #Find the device address using the "find_address()" function and put it below.
    #On Windows it is formatted as: "COMX" where X is a number.
    #On Linuxt it is formatted as: "/dev/ttyUSBX" where X is a number.
    #This method works only if the cabels are not moved, use with caution.
    Fixed_USB_port:
        CavroXE1000:
        CavroXCalibur:
        MXValve1:
        MXValve2:
        ThermoCube1:
        ThermoCube2:
        Oasis1:
        Oasis2:
        YoctoThermistor:
        TC720:
    #Pushbullet access tokens used for sending push messages to the user.
    #Make an account on: https://www.pushbullet.com/, goto settings, create and add.
    Operator_address:
        operator1:
        operator2:
        operator3:
        operator4:
        operator5:
        operator6:
        operator7:
        operator8:
        operator9:
        operator10:
    # ul between the valve and the target component.
    # For instance, to pump Hyb mix into the chamber the distance from the recevoir (valve) needs to be bridged.
    # The volume of the tubes running from the valve to the chamber is called the padding volume.
    # The pump will add the padding volume in SSC to the recevoir/syringe to push out so that all the Hyb mix reaches the 
    # Chamber without the tubes being filled with valuable Hyb mix.
    Padding:
        # Volume to the degasser
        Degass: 
        # Port 1-10 on valve 1
        P1: 
        P2: 
        P3:
        P4: 
        P5: 
        P6: 
        P7: 
        P8:
        P9: 
        P10: 
        # Port 1-10 on valve 2 are numberd 11-20. 
        # Measure full volume from the end of the recervoir on Valve1 to the target
        P11: 
        P12: 
        P13: 
        P14: 
        P15: 
        P16: 
        P17: 
        P18: 
        P19: 
        P20: 
    # Volume in ul below which the system will notifiy the user. 
    # If a connected buffer gets below the specified volume it will send a push message to the operator,
    # everytime the system checks for the buffer volumes.
    # For the "Waste", a message will be send if the volume is above the specified value.
    #
    Alert_volume:
        RunningBuffer: 
        # Port 1-10 on valve 1
        P1: 
        P2: 
        P3: 
        P4:
        P5: 
        P6:
        P7:
        P8:
        P9:
        P10:
        # Port 1-10 on valve 2 are numberd 11-20. 
        P11:
        P12:
        P13:
        P14:
        P15:
        P16:
        P17:
        P18:
        P19:
        P20:
        Disk: