Echo Export

Megastructures can be exported directly to an Echo liquid handler command sheet. A convenience function for generating a plate output visualization is also provided.

crisscross.core_functions.megastructure_composition ¶

visualize_output_plates ¶

visualize_output_plates(
    output_well_descriptor_dict,
    plate_size,
    save_folder,
    save_file,
    slat_display_format="pie",
    plate_display_aspect_ratio=1.495,
)

Prepares a visualization of the output plates for the user to be able to verify the design (or print out and use in the lab).

PARAMETER	DESCRIPTION
`output_well_descriptor_dict`	Dictionary where key = (plate_number, well), and the value is a list with: [slat_name, [category for all 32 handles on H2 side e.g. 0 2 3 4 0], [same for H5 side], slat_color, slat_type], where the categories are: 0 = control, 1 = assembly, 2 = seed, 3 = cargo, 4 = undefined
`plate_size`	Either 96 or 384
`save_folder`	Output folder
`save_file`	Output filename
`plate_display_aspect_ratio`	Aspect ratio to use for figure display - default matches true plate dimensions DEFAULT: `1.495`
`slat_display_format`	Set to 'pie' to output an occupancy pie chart for each well, 'barcode' to output a barcode showing the category of each individual handle, or 'stacked_barcode' for a more detailed view DEFAULT: `'pie'`

RETURNS	DESCRIPTION
	N/A

convert_slats_into_echo_commands ¶

convert_slats_into_echo_commands(
    slat_dict,
    destination_plate_name,
    output_folder,
    output_filename,
    reference_transfer_volume_nl=75,
    reference_concentration_uM=500,
    transfer_volume_multiplier_for_slats=None,
    source_plate_type="384PP_AQ_BP",
    output_empty_wells=False,
    manual_plate_well_assignments=None,
    unique_transfer_volume_for_plates=None,
    output_plate_size="96",
    center_only_well_pattern=False,
    generate_plate_visualization=True,
    plate_viz_type="stacked_barcode",
    destination_well_max_volume=25,
    normalize_volumes=False,
    color_output_wells=True,
)

Converts a dictionary of slats into an echo liquid handler command list for all handles provided.

PARAMETER	DESCRIPTION
`slat_dict`	Dictionary of slat objects
`destination_plate_name`	The name of the design's destination output plate
`output_folder`	The output folder to save the file to
`output_filename`	The name of the output file
`reference_transfer_volume_nl`	The default transfer volume for each handle (in nL) DEFAULT: `75`
`reference_concentration_uM`	The default concentration matching that of the selected transfer volume (in uM) DEFAULT: `500`
`transfer_volume_multiplier_for_slats`	Dictionary assigning a special transfer multiplier for specified slats (will be applied to all special plate volumes too) DEFAULT: `None`
`source_plate_type`	The physical plate type in use DEFAULT: `'384PP_AQ_BP'`
`output_empty_wells`	Outputs an empty row for a well if a handle is only a placeholder DEFAULT: `False`
`manual_plate_well_assignments`	The specific output wells to use for each slat (if not provided, the script will automatically assign wells). This can be either a list of tuples (plate number, well name) or a dictionary of tuples. DEFAULT: `None`
`unique_transfer_volume_for_plates`	Dictionary assigning a special transfer volume for certain plates (supersedes all other settings) DEFAULT: `None`
`output_plate_size`	Either '96' or '384' for the output plate size DEFAULT: `'96'`
`center_only_well_pattern`	Set to true to force output wells to be in the center of the plate. This is only available for 96-well plates. DEFAULT: `False`
`generate_plate_visualization`	Set to true to generate a graphic showing the positions and contents of each well in the output plates DEFAULT: `True`
`plate_viz_type`	Set to 'barcode' to show a barcode of the handle types in each well, 'pie' to show a pie chart of the handle types or 'stacked_barcode' to show a more in-detail view DEFAULT: `'stacked_barcode'`
`destination_well_max_volume`	The maximum total volume that can be transferred to a well in the output plate (in uL) DEFAULT: `25`
`normalize_volumes`	Set to True to normalize the volumes in each slat mixture (by adding water to the maximum volume) DEFAULT: `False`
`color_output_wells`	Set to True to add a color border to each well according to the slat's layer color or unique color (if available) DEFAULT: `True`

RETURNS	DESCRIPTION
	Pandas dataframe corresponding to output ech handler command list