Table 1 Open-3DULM: 3D localization and tracking parameters to be defined by the user
From: 3D transcranial ultrasound localization microscopy in awake mice: protocol and open-source pipeline
Open-3DULM parameters | Explanation | Values adopted in this work |
|---|---|---|
SVD filtering ([min_svd_value max_svd_value]) | The range of accepted singular values | 12–200 |
Bandpass filter ([left_cutoff_bandpass right_cutoff_bandpass]) and the order (filter_order) | The lower and upper-frequency bounds | not applied in this work |
Full-width-half-maximum (fwhm) | The size of the PSF of the microbubbles | [3 × 3 × 3] |
Patch size (patch_size) | The size of the 3D kernel where the local SNR is computed | [7 × 7 × 7] |
Minimum SNR (min_snr) | The minimum SNR value for a microbubble to be accepted | 9 |
Number of local maxima in the patch nb_local_max | The maximum number of allowed microbubbles inside a patch | 10 |
Number of particles (number_of_particles) | The number of microbubbles to be localized in every frame | 900 |
Maximum Velocity (mm/s) (max_velocity) | Maximum velocity in mm/s, which is converted into the maximum linking distance, i.e., the maximum allowed distance traveled by a particle between two frames | 30 mm/s |
Max Gap Closing (max_gap_closing) | The maximum number of frames that the microbubble is allowed to disappear and reappear | 0 |
Minimum Length (min_length) | The minimum number of frames a microbubble must be tracked for it to be accepted | 9 |
Resolution factor (res) | The hypothetical super-resolution factor | 10 |
