Profile Settings

WIA Driver - Use Windows Image Acquisition (WIA). This is a standard interface that most scanners support.
TWAIN Driver - Use TWAIN. This is an interface that is customized by the scanner manufacturer. Most scanners support it.

If you have issues with scanning, try switching between WIA and TWAIN. That will often solve scanning issues.

Device - Choose the scanner you want to use. If your scanner isn't listed, try switching between WIA and TWAIN or updating your scanner drivers.
Use predefined settings - Use the basic settings specified below. When you click Scan you won't have to do anything else.
Use native UI - Use the WIA/TWAIN interface. When you click Scan the interface will open and allow you to prepare for scanning.

Basic Settings

Paper Source - Whether to scan from Glass (flatbed), Feeder (automatic document feeder), or Duplex (feeder with duplex support).
Bit Depth - Whether to scan in Color, Grayscale, or Black & White.
Page Size - The size of the pages you're scanning. You can choose from the presets (A4, Letter, etc.) or make a custom page size.
Horizontal Align - Where the paper is positioned in the scanner (oriented assuming the paper is face down).
Resolution - How detailed the scan is, in DPI (dots per inch).
Scale - A scaling factor (can shrink the page 2x, 4x, or 8x).
Brightness - An adjustment for the brightness of the scan (-1000 to 1000).
Contrast - An adjustment for the contrast of the scan (-1000 to 1000).

Auto Save Settings

Enable Auto Save - Automatically save scans as they are performed to a predefined location (without having to manually click "Save PDF/Images").
Path - Where to save scans, including both a directory and file name with extension. Placeholders may be used to vary the file name based on number or date.
One file per page - Save a separate file for each page scanned.
One file per scan - If a feeder is used, save one file for each use of the feeder (possibly multiple pages).
Separate files by Patch-T - If a feeder is used, save one or more files for each use of the feeder, separated by Patch-T pages.
Clear images after saving - Don't load images into NAPS2 after they are auto saved. If not checked, scanned images may be saved multiple times (once by the auto save and then again by the user).

Advanced Settings

Image Quality

Maximum quality (large files) - Scan images losslessly. Good for PNG files, but documents can take up a lot of disk space.
Quality (0-100) - Scan images using JPEG compression with the provided quality. The default of 75 is good quality while also being space efficient.

The selected quality doesn't affect Black & White scans (since they are already space efficient at maximum quality).

Blank Pages

Exclude blank pages - Automatically skip blank pages when scanning, using the below parameters to determine whether a page is blank.
White Threshold - How bright a pixel is before it is considered "white".
Coverage Theshold - How much of the page must be "non-white" for it to be included. 0 = 0%, 100 = 1%.

If you have false positives (non-blank pages being skipped), decrease the Coverage Threshold. If you have false negatives (blank pages being included), increase the Coverage Threshold.

If you have both false positives and false negatives (or the Coverage Threshold is at its limit), change the White Threshold and try again to find a Coverage Threshold that works.

Compatiblity

Apply brightness/contrast after scan - If the brightness and/or contrast settings don't work for you, check this. It acts the same as if you change brightness/contrast from NAPS2's Image menu after scanning. Doesn't work with native UI.
Offset width based on alignment (WIA) - If part of the left side of your documents are cut off when using Left or Center alignments and WIA, this should fix it. Doesn't work with native UI.
Force matching page size - If the page size in your PDFs or printed pages is not what you expect, check this. Any further images scanned should then match your Page Size setting exactly. Doesn't work with native UI.
Flip duplexed pages - If the back sides of pages scanned with duplex are upside-down, check this.
Twain Implementation - If you have issues with TWAIN, you can try changing this.

Moving Profiles Across Computers

If you want to copy profiles and other settings to a different computer, you can manually copy the profiles.xml and config.xml files.

Windows

For installed versions of NAPS2, these files are located in this folder:

%APPDATA%\NAPS2\

For example, if your Windows username is John, it would be:

C:\Users\John\AppData\Roaming\NAPS2\

For portable versions of NAPS2, they are located in the Data folder.

Mac

On Mac, these files are located in this folder:

~/.config/naps2/

For example, if your username is "john", it would be:

/Users/john/.config/naps2/

To access that folder from Finder, click "Go" → "Computer", browse to /Users/john, then press "Cmd+Shift+." to show the hidden ".config" folder.

Linux

On Linux, these files are located in this folder:

~/.config/naps2/