Import Movies
or Import Micrographs
jobs to indicate that you are processing negative stain data (light-on-dark). Subsequent jobs that use the imported negative stain data, will adjust their relevant parameters accordingly (for more details, see below: Jobs affected by negative stain data).Import Particles
job. Subsequent jobs that use the imported negative stain data, will adjust their relevant parameters accordingly (for more details, see below: Jobs affected by negative stain data).Import Movies
: "Negative Stain" toggle will set mscope_params/neg_stain
field to 1
(True)Import Micrographs
: "Negative Stain" toggle will set mscope_params/neg_stain
field to 1
(True)Import Particles
: "Data Sign" drop-down list will set blob/sign
field to +1
(cryo-EM data) if dark-on-light
is selected or -1
(negative stain data) if light-on-dark
is selected. The default is light-on-dark
, as cryo-EM data is usually inverted during processing.Exposure Tools
: Allows user to set mscope_params/neg_stain
and mscope_params/phase_plate
manually.Manual Picker
: Extracted particles are indicated with the correct sign (+1 for dark-on-light particles and -1 for light-on-dark particles)Template Picker
: Templates used to pick particles are flipped (dark-on-light to light-on-dark)Blob Picker
: Blob templates used to pick particles are flipped (dark-on-light to light-on-dark)Local Motion
: Extracted particles are indicated with the correct sign (+1 for dark-on-light particles and -1 for light-on-dark particles)Extract From Micrographs
: Extracted particles are indicated with the correct sign (+1 for dark-on-light particles and -1 for light-on-dark particles)Topaz Train
: Preprocessed micrographs are inverted (light-on-dark to dark-on-light) before being used for model trainingTopaz Extract
: Input micrographs are inverted (light-on-dark to dark-on-light) before being processed by Topaz Extract