Current code can be inefficient with large image stacks so I will be making the file processing more efficient.
This script requires Napari to be installed.
To launch the script open Napari conda enviroment and navigate to directory where the script is located.
The script can be called using python nlts.py <directory location> <channel1,channel2,...> <optional arguments>
There are several optional image setting that can be passed into the script before launch. When passing in an argument that requires multiple values seperate them by spaces (e.g --contrast_limits 0.0 100.0 0.0 100.0) in the case of numerical inputs, or commas (e.g --colormaps blue,green) in the case of strings.
- opacity: (0.0-1.0) The opacity of the image. One for each channel.
- contrast limits: (No limits) The upper and lower contrast limits of the image. Upper and lower bounds for each image.
- gamma: (0.0-2.0) The gamma correct of the image. One for each channel.
- colormaps: The desired colormap for each channel.
- blending: Blending option for each channel. Default is additive.
- interpolation: Interpolation option for each channel. Default is nearest
- fetch interval: Duration (seconds) to wait between searching directory for new images. Default is 2 minutes
- layer buffer: Can prevent the files from being loaded into Napari in the wrong order in some rare cases, so we leave out the last N layers to prevent this. (This is not working as intended currently.