Aydin CLI Tutorials

We have few CLI tutorials below to demonstrate how to use various features of the CLI Aydin provides.

Checking if Aydin CLI can read and interpret your image right

You can use the following line to get information about how Aydin will be interpreting their image file.

$ aydin info image.tif

├╗ Reading image file at: /PATH/TO/IMAGE/image.tif
│├ Reading file /PATH/TO/IMAGE/image.tif as TIF file
│├ Metadata:  is_folder=False, ext=tif, axes=YX, shape=(321, 481), batch_axes=(False, False), channel_axes=(False, False), dtype=uint8, format=tif
│┴« 4.24 milliseconds
│

Viewing your image with Aydin CLI

You can use the following line to view their image with help of integrated napari in Aydin CLI.

$ aydin view image.tif

Note: aydin view command would work as expected only on the machines with screen access.

Denoising a single image

You can use the following line to denoise a single image with default options.

$ aydin denoise image.tif

Denoising a single image with customized options

We have made it possible for users to play with various parameters and options related to the denoising approach they have chosen and save their specific set of parameters into a JSON file. We also made it possible to pass such JSON file to Aydin CLI. One can achieve this as shown below:

$ aydin denoise image.tif --lower-level-args=image_options.json

Denoising a single image with a pre-trained Aydin model

You can use the following line to denoise a single image with a pre-trained Aydin model. You can use the Aydin Studio GUI to play with different parameters and train a model to pass here to the Aydin CLI.

$ aydin denoise image.tif --model-path=image_model.zip --use-model

Denoising multiple image files

You can use the following line to denoise multiple image files with default options:

$ aydin denoise image1.tif image2.tif image3.tif

Or alternatively one can use glob patterns such as:

$ aydin denoise image*.tif

Deconvolving a single image

You can use the following line to deconvolve a single image with default options.

$ aydin lucyrichardson image.tif

Using your PSF to deconvolve your image

You can use the following line to deconvolve a single image with default options and their own psf. Passed psf file assumed to be a single psf image in a lossless format.

$ aydin lucyrichardson image.tiff psf.tif

Choosing the computational backend

You can use the following line to denoise or deconvolve a single image with their choice of computational backend.

$ aydin denoise image.tif --backend="noise2selffgr-nn"
$ aydin lucyrichardson image.tif --backend="cupy"