diff --git a/tools/plantseg/.shed.yml b/tools/plantseg/.shed.yml new file mode 100644 index 00000000..0a88a9b9 --- /dev/null +++ b/tools/plantseg/.shed.yml @@ -0,0 +1,8 @@ +categories: + - Imaging +description: Tool for cell instance aware segmentation in densely packed 3D volumetric images +long_description: PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. +name: plantseg +owner: imgteam +homepage_url: https://github.com/bmcv +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/plantseg/ diff --git a/tools/plantseg/create-config.py b/tools/plantseg/create-config.py new file mode 100644 index 00000000..410e1b44 --- /dev/null +++ b/tools/plantseg/create-config.py @@ -0,0 +1,34 @@ +import argparse +import json + +import yaml + + +# This script genereates the config file required by PlantSeg. +# For an overview of the config fields, see: +# https://github.com/kreshuklab/plant-seg/blob/master/examples/config.yaml + + +if __name__ == '__main__': + + parser = argparse.ArgumentParser() + parser.add_argument('--inputs', type=str, help='Path to the inputs file', required=True) + parser.add_argument('--config', type=str, help='Path to the config file', required=True) + parser.add_argument('--img_in', type=str, help='Path to the input image', required=True) + args = parser.parse_args() + + with open(args.inputs, 'r') as fp: + inputs = json.load(fp) + + cfg = dict(path=args.image) + for section_name in ( + 'preprocessing', + 'cnn_prediction', + 'cnn_postprocessing', + 'segmentation', + 'segmentation_postprocessing', + ): + cfg[section_name] = inputs[section_name] + + with open(args.config, 'w') as fp: + fp.write(yaml.dump(cfg)) diff --git a/tools/plantseg/creators.xml b/tools/plantseg/creators.xml new file mode 120000 index 00000000..5d2b71e0 --- /dev/null +++ b/tools/plantseg/creators.xml @@ -0,0 +1 @@ +../../macros/creators.xml \ No newline at end of file diff --git a/tools/plantseg/plantseg.xml b/tools/plantseg/plantseg.xml new file mode 100644 index 00000000..e60bb49c --- /dev/null +++ b/tools/plantseg/plantseg.xml @@ -0,0 +1,86 @@ + + with PlantSeg + + creators.xml + tests.xml + 1.8.1 + 0 + + + + + + operation_3443 + + + plantseg + + + plant-seg + pytorch + bioimageio.spec + pyyaml + + + + + + + + + + + +
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+ + + + + + + + + + + + + + **Perform segmentation in densely packed 3-D volumetric images.** + + PlantSeg is a tool for cell instance aware segmentation in densely packed 3D volumetric images. + The pipeline uses a two stages segmentation strategy (Neural Network + Segmentation). + The pipeline is tuned for plant cell tissue acquired with confocal and light sheet microscopy. + + + + 10.7554/eLife.57613 + + diff --git a/tools/plantseg/test-data/sample_ovule.h5 b/tools/plantseg/test-data/sample_ovule.h5 new file mode 100644 index 00000000..130fbeb5 Binary files /dev/null and b/tools/plantseg/test-data/sample_ovule.h5 differ diff --git a/tools/plantseg/test-data/sample_ovule_output.h5 b/tools/plantseg/test-data/sample_ovule_output.h5 new file mode 100644 index 00000000..4cda55b2 Binary files /dev/null and b/tools/plantseg/test-data/sample_ovule_output.h5 differ diff --git a/tools/plantseg/tests.xml b/tools/plantseg/tests.xml new file mode 120000 index 00000000..e20d710a --- /dev/null +++ b/tools/plantseg/tests.xml @@ -0,0 +1 @@ +../../macros/tests.xml \ No newline at end of file