General Preferences: Imaging
These options control the opening and display of imported images.
Image File Reading and Writing Protocol
Use these options to control the generation of configuration files.
- When writing image files...: MBF-specific information includes data about the Data DIB, Display DIB, and other information about the image file and how Neurolucida should process it.
- When saving...: Adjustments are saved in a separate file to avoid modifying the image.
Extended image data maintained in memory
Every time an image is modified, extended image data changes. In most situations, All unsaved is preferable.
When Image Bit Depth is Unknown
These options provide you with options to improve the display of your image when Neurolucida is unable to identify the bit depth.
Why does it matter?
When a high bit depth (greater than 8) image is loaded, the display may not be optimal for visualization because the image contains a broad range of values (e.g., 65536 values for a 16-bit image) while the monitor is only set to display up to 256 values (8-bit depth range). As a result, Neurolucida maps the pixel range into a smaller color intensity range.
In addition, the pixel values in the image file are typically expressed in 16-bit values although the image may have been generated by a 12 or 14-bit camera. As a result, some of the bits of this image may be expressed as 0.
Bit Depth Settings
Remember that your choice for bit depth only affects the display of the image, not the underlying data.
Use Max Pixel
Neurolucida selects the lowest bit depth that includes the highest pixel value found within the image.
Example:
If the highest pixel value found in the image is 3965, then the minimum bit depth that could include this value is 12 since the range for a 12-bit image is 0-4096. Neurolucida will use 12 as the bit depth.
12 may not be the actual bit depth range of the image (i.e., the image could have been created in a 16-bit image space), but the maximal pixel value contained with that image is still 3965.
Use “x” bits per pixel
If you know the full bit depth range for the image, select it from the drop-down menu.
Always Ask
When selected, the Unknown Bit Depth window is displayed when opening the image. 
White Point
By setting the white point (i.e., the value associated with the white color), you can refine the range of values to be mapped for the display.
Maximum allowed by bit depth
The white point is associated with the maximal value of the range.
Example: If you selected 12 as the bit depth, the white point is associated with 4095 and the range is 0-4096.
Maximum pixel of image(s)
Neurolucida identifies the maximum pixel value in the image and associates it with the white point. Doesn't depend on bit depth and may result in a narrower range than the bit depth range.
Example: If 12 is the bit depth, the white point might be associated with 3200, which is lower than the maximum pixel value for a 12 bit depth (4096). 3200 is used as the white point value.
Black Point
By setting the black point (i.e., the value associated with the black color), you can refine the range of values to be mapped for the display.
0 (Min. allowed by bit depth)
The black point is associated with the minimal value of the range, which is 0.
Minimum pixel of image(s)
Neurolucida identifies the minimum pixel value in the image and associates it with the black point. Doesn't depend on bit depth.
Example: Neurolucida identifies the minimal pixel value as 120 instead of 0. 120 is used as the black point value.
Other settings
False Color Single Channel Images
Select when working with single-channel images requiring false coloring.
Image Averaging
Acquires n images and averages these n acquisitions into a single image. Use this option if your camera generates a lot of noise in the image.
Number of images to use: Start with a small number and gradually increase until the noise reduction is satisfactory.
Load All Stacks At Same Z
If left unchecked, image stacks are loaded with the first image at the current Z position, with the images in the stack placed at regular intervals in Z from the first image.
Marquee Around Current Image
Useful to identify the current image.
Alternative method: Use the Image Organizer; the current image is identified by a blue highlight for the image information.
Reader Channel Colors
Displays the Image File Reader Channel Colors dialog box.
Use with multichannel image files that don't contain color specifications (e.g., Nikon IDS/ICS files) to assign colors to display.
Remove Off-Screen Image Stacks From Memory
May decrease the memory load due to large image stacks by only using memory for images that are currently being displayed. If this option is enabled, the images that make up an image stack are unloaded from memory when:
- The image stack has not been modified since being loaded.
- The image stack is not visible in the current field of view.
- The image stack is not selected in the Image Organizer.
The image stack is reloaded when:
- The image stack is selected in the Image Organizer.
- The image stack is moved to appear in the current field of view.
Save when acquired
Save Images when they are acquired: Select to automatically save the acquired images to a defined path.
Optional: Use a base name. As each image is saved, Neurolucida uses the base name and a number that increments by 1.
Select Color Filters with F9-F12 / Toggle Color Filters with F9-F12
Color filters can be either selected or toggled with the function keys F9-F12. If using the function keys to select a filter, only the color filter selected is used when that function key is pressed. If function keys are used to toggle filters, multiple filters can be used at the same time in variable combinations. Function keys are assigned as follows: F9=none, F10=red, F11=green, F12=blue.
Show Images in Where Is mode
When checked, the acquired and imported image thumbnails are shown in their appropriate locations in Where Is mode.
Turn Off Preview on Apply
Affects the viewing of Image Processing effects. If this option is checked, the preview area will disappear after an Image Processing effect has been applied. It can be turned back on by checking the Preview box in the Image Processing dialog box.
Turn On Preview On New Effect
his option affects the viewing of Image Processing. If this option is checked, a preview window automatically appears whenever a new image Processing effect is selected.