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Generally, betwen 5A and 3A is best.", "order": 8, "section": "motion_settings", "advanced": false, "hidden": false }, "bfactor": { "type": "number", "value": 500, "title": "B-factor during alignment", "desc": "B-factor that blurs frames before aligning. Generally 500 to 100 is best.", "order": 9, "section": "motion_settings", "advanced": false, "hidden": false }, "frame_start": { "type": "number", "value": 0, "title": "Start frame (included, 0-based)", "desc": "Which frame number, starting at zero, to begin motion correction from. This value controls how many early frames are dropped from the motion corrected result. This value will also be used in local motion correction.", "order": 10, "section": "motion_settings", "advanced": false, "hidden": false }, "frame_end": { "type": "number", "value": null, "title": "End frame (excluded, 0-based) ", "desc": "Which frame number, starting at zero, to not include in motion correction, also excluding all frames after this one. Generally this does not improve results, as later frames are downweighted during dose weighting in local motion correction.", "order": 11, "section": "motion_settings", "advanced": false, "hidden": false }, "output_fcrop_factor": { "type": "enum", "value": "1", "title": "Output F-crop factor", "desc": "Output Fourier cropping factor. 1.0 means no cropping, 1/2 means crop to 1/2 the resolution, etc.", "order": 12, "section": "motion_settings", "advanced": false, "hidden": false, "enum_keys": [ "1", "3/4", "1/2", "1/4", "1/8", "1/16" ], "enum_dict": { "1": 1.0, "3/4": 0.75, "1/2": 0.5, "1/4": 0.25, "1/8": 0.125, "1/16": 0.0625 } }, "override_total_exp": { "type": "number", "value": null, "title": "Override e/A^2", "desc": "Override the dose (in total e/A^2 over the exposure) that was given at import time but can be overridden here.", "order": 13, "section": "motion_settings", "advanced": false, "hidden": false }, "variable_dose": { "type": "boolean", "value": false, "title": "Allow Variable Dose", "desc": "Enable correct processing when frames have variable dose fractionation", "order": 14, "section": "motion_settings", "advanced": true, "hidden": false }, "smooth_lambda_cal": { "type": "number", "value": 0.5, "title": "Calibrated smoothing", "desc": "Calibrated smoothing constant applied to trajectories", "order": 15, "section": "motion_settings", "advanced": true, "hidden": false }, "override_K_Z": { "type": "number", "value": null, "title": "Override knots Z", "desc": "Override automatically selected spline order for Z dimension (time)", "order": 16, "section": "motion_settings", "advanced": true, "hidden": false }, "override_K_Y": { "type": "number", "value": null, "title": "Override knots Y", "desc": "Override automatically selected spline order for Y dimension (vertical)", "order": 17, "section": "motion_settings", "advanced": true, "hidden": false }, "override_K_X": { "type": "number", "value": null, "title": "Override knots X", "desc": "Override automatically selected spline order for X dimension (horizontal)", "order": 18, "section": "motion_settings", "advanced": true, "hidden": false }, "random_seed": { "type": "number", "value": 834184743, "title": "Random seed", "desc": "Use a fixed random seed for hot pixel replacement.", "order": 19, "section": "random", "advanced": true, "hidden": false }, "compute_num_gpus": { "type": "number", "value": 1, "title": "Number of GPUs to parallelize", "desc": "Number of GPUs over which to parallelize computation.", "order": 20, "section": "compute_settings", "advanced": false, "hidden": false } }, "params_secs": { "general_settings": { "title": "General settings", "desc": "", "order": 0 }, "motion_settings": { "title": "Motion correction", "desc": "", "order": 1 }, "random": { "title": "Random Seeds", "desc": "", "order": 2 }, "compute_settings": { "title": "Compute settings", "desc": "", "order": 3 } }, "params_spec": { "compute_num_gpus": { "value": 4 } }, "parents": [ "J1" ], 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