Q: How do I monitor my dose on my direct detection camera?

Follow these steps: Locate the blue status bar at the bottom of the DigitalMicrograph software window. Read the dose information displayed: Electrons per pixel per second (e-/s): Useful for setting the optimal dose rate for the counting algorithm. Dose rate (e - /Å²/s): Indicates the rate at which electrons are delivered to the sample area. Total dose (e - /Å²): Shows the cumulative dose received by the sample with the image settings you have chosen on the camera. Tip: Use these readings to set and monitor the dose for your experiment, ensuring optimal image quality and sample preservation.

Q: How can I capture and save my data as *.tiff or *.mrc formats in DigitalMicrograph?

Follow these steps: Open the Data Set palette in DigitalMicrograph. Go to the Image Name Setup option. Choose a filepath where you want to save your data. Select your desired image format (e.g., *.tiff, *.mrc) in the File Content and Format section of the dialog. Enable Save After Acquire in the Data Set palette. Capture images with the camera.

Q: I see strange features in my camera image that do not go away. What do I do?

Step-by-step instructions: Enable Power User mode: Go to the top menu bar and select Help \ User Mode \ Power User to enable. Take new dark references: Go to the top menu bar and select Camera \ Prepare Dark Reference. Follow the instructions to acquire. Take new gain references: Go to the top menu bar and select Camera \ Prepare Gain Reference. Follow the instructions to acquire. Check your image again: After updating both references, capture a new image and see if the strange features are resolved. If the issue persists: Contact Gatan service for expert assistance. Tip: Regularly updating dark and gain references can prevent many common imaging artifacts. If you continue to see unexplained features, there may be a hardware or software issue that requires professional support.

Q: How can I acquire my single particle cryo-EM data in an automated fashion using DigitalMicrograph?

Gatan offers Latitude ® S software that enables automated single particle data acquisition using your Gatan camera. See the Latitude S software page for more information. The full Latitude suite also enables automated data acquisition of imaging tomography data, as well as diffraction tomography data (aka Micro ED / 3DED): Latitude D software

Q: Can I use my K3 camera for both single particle cryo-EM AND MicroED/3DED experiments?

Yes, the K3 ® camera is fully capable of capturing high-quality imaging and diffraction data to support multiple cryo-EM techniques. See this application note for more instruction on how to set up your diffraction experiment: Acquiring counted electron diffraction data without a beam stop with Gatan electron counting direct detector .

Question 1

How do I monitor my dose on my direct detection camera?

Accepted Answer

Follow these steps:

Locate the blue status bar at the bottom of the DigitalMicrograph software window.
Read the dose information displayed:
- Electrons per pixel per second (e-/s): Useful for setting the optimal dose rate for the counting algorithm.
- Dose rate (e^-/Å²/s): Indicates the rate at which electrons are delivered to the sample area.
- Total dose (e^-/Å²): Shows the cumulative dose received by the sample with the image settings you have chosen on the camera.

Tip: Use these readings to set and monitor the dose for your experiment, ensuring optimal image quality and sample preservation.

Question 2

How do I enable correlated double sampling (CDS) mode on my direct detection camera?

Accepted Answer

Follow these steps in DigitalMicrograph:

Open the camera palette.
Click the setup menu (gear icon) to open the camera settings dialog.
Locate the option for CDS mode.
- Select whether you want to enable or disable CDS mode.
Other available options (may vary by camera model):
- Enable dark mode for diffraction experiments.
- Choose between acquiring gain normalized images or unprocessed images.

Question 3

How can I capture and save my data as *.tiff or *.mrc formats in DigitalMicrograph?

Accepted Answer

Follow these steps:

Open the Data Set palette in DigitalMicrograph.
Go to the Image Name Setup option.
Choose a filepath where you want to save your data.
Select your desired image format (e.g., *.tiff, *.mrc) in the File Content and Format section of the dialog.
Enable Save After Acquire in the Data Set palette.
Capture images with the camera.

Question 4

I see strange features in my camera image that do not go away. What do I do?

Accepted Answer

Step-by-step instructions:

Enable Power User mode: Go to the top menu bar and select Help \ User Mode \ Power User to enable.
Take new dark references: Go to the top menu bar and select Camera \ Prepare Dark Reference. Follow the instructions to acquire.
Take new gain references: Go to the top menu bar and select Camera \ Prepare Gain Reference. Follow the instructions to acquire.
Check your image again: After updating both references, capture a new image and see if the strange features are resolved.
If the issue persists: Contact Gatan service for expert assistance.

Tip: Regularly updating dark and gain references can prevent many common imaging artifacts. If you continue to see unexplained features, there may be a hardware or software issue that requires professional support.

Question 5

How can I acquire my single particle cryo-EM data in an automated fashion using DigitalMicrograph?

Accepted Answer

Gatan offers Latitude^® S software that enables automated single particle data acquisition using your Gatan camera. See the Latitude S software page for more information.
The full Latitude suite also enables automated data acquisition of imaging tomography data, as well as diffraction tomography data (aka Micro ED / 3DED): Latitude D software

Question 6

Can I use my K3 camera for both single particle cryo-EM AND MicroED/3DED experiments?

Accepted Answer

Yes, the K3^® camera is fully capable of capturing high-quality imaging and diffraction data to support multiple cryo-EM techniques. See this application note for more instruction on how to set up your diffraction experiment: Acquiring counted electron diffraction data without a beam stop with Gatan electron counting direct detector.

Cryo-electron microscopy (Cryo-EM) FAQs

How do I monitor my dose on my direct detection camera?

How do I enable correlated double sampling (CDS) mode on my direct detection camera?

How can I capture and save my data as .tiff or .mrc formats in DigitalMicrograph?

I see strange features in my camera image that do not go away. What do I do?

How can I acquire my single particle cryo-EM data in an automated fashion using DigitalMicrograph?

Can I use my K3 camera for both single particle cryo-EM AND MicroED/3DED experiments?