You can specify the data is negative stain, at the time of import, or manually.
When importing negative stain movies or micrographs, use the Negative Stain Data toggle in the 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).
If importing particles, specify the type of data being imported in the 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).
Use the Exposure Tools job to manually set the Negative Stain and Phase Plate Data values for an exposure dataset:
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 training
Topaz Extract
: Input micrographs are inverted (light-on-dark to dark-on-light) before being processed by Topaz Extract
NB. Certain jobs plot particles while taking into account their particle sign (+1 for dark-on-light (cryo-EM data) and -1 for light-on-dark (negative stain data)). You might notice that your negative stain data looks like cryo-EM data in the plot, but please note that the actual particles on disk are still negative stain data.
Data Type | Data Sign | Description |
Cryo-EM | +1 | dark-on-light |
Negative Stain | -1 | light-on-dark |
Note: Cryo-EM data is typically recorded as +1 (dark-on-light) but is often inverted during processing.
​