Color code key: Orange text: customized Blue text: fixed

Use Cases:

1. Actively collecting data and checking the results on-the-fly.
2. After data collection.

Inputs needed before running:

1. Directory with raw uncorrected frames

2. Gain reference MRC file

3. Motioncor2 executable (requires installation)

   Download page: https://emcore.ucsf.edu/ucsf-software

4. MotionCor parameters for your dataset

Output you will get:

Root directory

— MotionCorrection:

— MotionCor:

— corrected_images: folder storing motion-corrected images

— Raw_Frames_Do_Not_Delete

• This is your original data, do not delete them before backing up!
• If need to redo the Motion correction, please move the original data out of this folder.

Explanation for each of the required fields in the GUI (see Fig. 1).

• “Raw Frames Folder”: the path to the directory where raw images are stored, normally the stacked tif frames. No default value.
• “MotionCor Executable”: the path to the motion correction software. No default value.
• “Gain Reference Image”: the path to your gain reference file, typically an MRC file. No default value.
  • you have to transfer from DM4 format to MRC