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Bryan Ellerbrock edited this page Oct 4, 2021 · 9 revisions

Automated Image Analysis

Introduction

Images stored in Breedbase can be subjected to automated analyses using a standardized protocol and store the results, usually keyed to a trait, into the database.

User interface

The user interface to submit images to analysis is available on Breedbase at the URL /tools/image_analysis.

Images can be queried and selected from a list

image_analysis_select

Then users can pick an analysis service to submit them to

image_analysis_submit

The analysis services are currently defined in mason/tools/image_analysis.mas. This should be refactored into an entry in sgn_local.conf.

Analysis progress is reported

image_analysis_progress

Then results are displayed for review, with the option to save the scores as new phenotypes.

image_analysis_results

Backend implementation

JSON call format

The structure of the call is defined as follows:

my $resp = $ua->post(
      "http://unet.mcrops.org/api",
      Content_Type => 'form-data',
      Content => [
          image => [
            '/home/production/volume/public/images/image_files_test/5b/73/32/47/f52d22ee4227e1c9049ef4b8/image-3.png',
            Content_Type => 'image/png'
          ],
      ]
    );

JSON return format

{
               'image_name' => 'Sr9GHXyXCN_nrVV13r.JPG',
               'trait_value' => '33.75',
               'image_link' => 'http://unet.mcrops.org/api_results/Sr9GHXyXCN_nrVV13r.png',
               'trait_name' => 'CBSDpct | CO_334:0002078'
};
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