Ratio Output Process Description

Ratio Output Process Description:

This process allows you to export the ratio images you have created in step 10 (or step 11, if photobleach correction has been applied) as 32 bit .tif images.

Parameter Descriptions:

Ratio Channel:

This box allows you to select the channel which is the NUMERATOR of the ratio images you want to export (usually the FRET channel).

TIF export options:

Customize color limits

If checked, it enables the "color limits options" panel, and allows you to manually specify the color scale of the ratio output tiff images.

Color limits options:

Manually set percentage of lower and upper color limits

If checked, it allows you to manually specify the color scale limits by percentage. If unchecked, it enables the "manually set color limits by values" panel, allowing you to manually specify the lower and upper color scale limit values.

Lower color limit %:

This allows you to specify the lower color scale percentage. For example, setting this to 5% will replace the bottom 5% of data in the color scale range with the new minimum.

Upper color limit %:

This allows you to specify the upper color scale percentage. For example, setting this to 99% will replace the top 1% of data in the color scale range with the new maximum.

Lower color limit value:

This allows you to specify the lower bound of the color scale. The value can go lower than the lowest color scale value across all ratio output images, to facilitate batch analysis across multiple movies.

Upper color limit value:

This allows you to specify the upper bound of the color scale. The value can go higher than the highest color scale value across all ratio output images, to facilitate batch analysis across multiple movies.

Select Path:

This allows you to specify the directory to save the .tif ratio images to. They will be saved to a subdirectory of this folder called "ratio_tiffs", with one .tif file per ratio image.

Make ratio movie:

This allows you to export the ratio output as a movie (in .avi and/or .mov format).

Movie options:

Use a constant scale throughout the movie:

If checked, the customized color scale set above will be used throughout the movie. If the color limits are not manually set, the constant scale will be based on the overall minimum and maximum intensity values across all output images. If unchecked, the range will be selected separately for each frame.

Display color bar:

If checked, a bar showing the color scale, i.e., the ratio value associated with each color in the movie, will be displayed.

Create .avi/.mov movie:

If checked, the movie will be saved as a .avi/.mov.