diff --git a/mantis/acquisition/settings/example_acquisition_settings.yaml b/mantis/acquisition/settings/example_acquisition_settings.yaml index 6922df4e..fed0f16f 100644 --- a/mantis/acquisition/settings/example_acquisition_settings.yaml +++ b/mantis/acquisition/settings/example_acquisition_settings.yaml @@ -32,7 +32,16 @@ lf_slice_settings: z_stage_name: 'MCL Piezo' z_start: -10 z_end: 10 - z_step: 0.4 + # When using 0.52 NA transmission light illumination, Nyquist sampling of the + # axial dimension will be achieved by using (450*1.4)/(1.35^2 + 0.52^2) = 300 nm + # steps in sample space. We can achieve this by using (300 nm)*1.4/2 = 210 nm + # steps of the mirror due to the 1.4x magnification of the remote volume and the + # fact that the optical path length is extended by twice the mirror's motion. + # + # Here we choose to oversample the data to match the light-sheet axial + # sampling. After deskewing and 3x binning, the light-sheet samples are + # spaced by ~205 nm, so we choose (205 nm)*1.4/2 = 143 nm mirror steps. + z_step: 0.143 use_sequencing: True # Define channel settings for the light-sheet acquisition. Channels may have @@ -46,8 +55,13 @@ ls_channel_settings: # Define slice (i.e. z-stack) settings for the light-sheet acquisition. ls_slice_settings: z_stage_name: 'AP Galvo' - z_start: -2.5 # in Volts - z_end: 2.5 # 5V range corresponds to 155 um scan range + # 5.5 V range corresponds to 170 um scan range which matches the label-free + # field of view + z_start: -2.75 # in Volts + z_end: 2.75 + # Nyquist sampling of this dimensions will be achieved by using 3.75 mV steps + # (corresponding to ~116 nm). When imaging live cells we chose to undersample + # this dimension to decrease photobleaching and photodamage. z_step: 0.01 # 10 mV is equivalent to 310 nm use_sequencing: True