Sdeconv2d

List versions

Description

2D image deconvolution using sparse variation model. This deconvolution algorithm is designed for images with low signal like microscopy images:

Original image Deconvolution

The full documentation is avalable here

Parameters

They are three main parameters to tune:

  1. sigma: the sigma (width) of the Gaussian model PSF
  2. regularization: the regularization parameter. It is the weight of the model w.r.t the data term
  3. weighting: the model weight in [0, 1]. Recommended values a 0.1 for sparse image, 0.9 for regular images and 0.6 for compromize

More details are avalable here

Command

To run the deconvolution in the AllGo interface:

  1. Upload your input file:

  2. Set the command line in the parameters input (change the values with your settings):

    -i name_of_your_input_image.tif -o output.tif -sigma 2 -regularization 11 -weighting 0.6

In order to run a job you need to be identified or register a new account.

API Reference

The following curl command will create a job (note: job[webapp] is required, all other parameters are optional):

curl -H 'Authorization: Token token=<your private_token>' \
    -X POST https://allgo18.inria.fr/api/v1/jobs \
    -F 'job[webapp]=svdeconv' \
    -F 'job[version]=1.0.0' \
    -F 'job[param]=' \
    -F 'job[queue]=standard' \
    -F 'files[0]=@test.txt' \
    -F 'files[1]=@test2.csv'
Bash

Monitor its progress:

curl -H 'Authorization: Token token=<your private_token>' \
    https://allgo18.inria.fr/api/v1/jobs/JOB_ID/events
Bash

Get the result:

curl -H 'Authorization: Token token=<your private_token>' \
    https://allgo18.inria.fr/api/v1/jobs/JOB_ID
Bash

Abort the job:

curl -H 'Authorization: Token token=<your private_token>' \
    -X POST https://allgo18.inria.fr/api/v1/jobs/JOB_ID/abort
Bash

Delete the job:

curl -H 'Authorization: Token token=<your private_token>' \
    -X DELETE https://allgo18.inria.fr/api/v1/jobs/JOB_ID
Bash