Tutorial: Negative Stain Data

How to specify negative stain data
You can specify the data is negative stain, at the time of import, or manually.
Import negative stain movies or micrographs
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).
Import negative stain particles
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).
Manually set negative stain values for an exposure dataset
Use the Exposure Tools job to manually set the Negative Stain and Phase Plate Data values for an exposure dataset:
Jobs and parameters affected by negative stain data
1.
Import Movies: "Negative Stain" toggle will set mscope_params/neg_stain field to 1 (True)
2.
Import Micrographs: "Negative Stain" toggle will set mscope_params/neg_stain field to 1 (True)
3.
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.
4.
Exposure Tools: Allows user to set mscope_params/neg_stain and mscope_params/phase_plate manually.
5.
Manual Picker: Extracted particles are indicated with the correct sign (+1 for dark-on-light particles and -1 for light-on-dark particles)
6.
Template Picker: Templates used to pick particles are flipped (dark-on-light to light-on-dark)
7.
Blob Picker: Blob templates used to pick particles are flipped (dark-on-light to light-on-dark)
8.
Local Motion: Extracted particles are indicated with the correct sign (+1 for dark-on-light particles and -1 for light-on-dark particles)
9.
Extract From Micrographs: Extracted particles are indicated with the correct sign (+1 for dark-on-light particles and -1 for light-on-dark particles)
10.
Topaz Train: Preprocessed micrographs are inverted (light-on-dark to dark-on-light) before being used for model training
11.
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 reference chart
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.
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Case Study: Processing EMPIAR-10291 (300 Micrographs) to 3.4Å in 1 hour 25 minutes

Tutorial: Phase Plate Data

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Contents

How to specify negative stain data

Import negative stain movies or micrographs

Import negative stain particles

Manually set negative stain values for an exposure dataset

Jobs and parameters affected by negative stain data

Data type reference chart