| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.25.2+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.25.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.14.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1-2 |
| toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.1.1 |
| toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.0.9 |
| toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.0.8 |
| ip_2d_feature_extraction |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| scikit-image | 0.25.2 | package |
| pandas | 2.2.2 | package |
| giatools | 0.7.3 | package |
| ome-zarr | 0.12.2 | package |
| Additional information about this tool |
python '$__tool_directory__/2d_feature_extraction.py'
#if $labels.extension == "zarr"
--labels '$labels.extra_files_path/$labels.metadata.store_root'
#else
--labels '$labels'
#end if
#if $setup.mode == "with-intensities"
#if $setup.intensities.extension == "zarr"
--intensities '$setup.intensities.extra_files_path/$setup.intensities.metadata.store_root'
#else
--intensities '$setup.intensities'
#end if
#end if
--output '$output'
--params '$params'
--verbose
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
labels: input/input12.png setup|features: ['label', 'area', 'area_convex', 'solidity'] setup|mode: without-intensities |
name: value |
input/input12.png value |
| Test-2 |
labels: input/input11.tiff setup|intensities: input/input1_uint8.tiff setup|features: ['area', 'mean_intensity', 'perimeter'] setup|mode: with-intensities |
name: value |
input/input11.tiff input/input1_uint8.tiff value |
| Test-3 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: area setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-4 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: area_convex setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-5 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: area_filled setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-6 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: axis_major_length setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-7 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: axis_minor_length setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-8 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: bbox setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-9 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: centroid setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-10 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: eccentricity setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-11 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: equivalent_diameter_area setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-12 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: euler_number setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-13 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: extent setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-14 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: inertia_tensor_eigvals setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-15 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: moments setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-16 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: moments_hu setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-17 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: orientation setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-18 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: perimeter setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-19 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: solidity setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-20 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: max_intensity setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-21 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: mean_intensity setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-22 |
labels: input/input13.zarr setup|intensities: input/input1_uint8.tiff setup|features: min_intensity setup|mode: with-intensities |
name: value |
input/input13.zarr input/input1_uint8.tiff value |
| Test-23 |
labels: input/input9.zarr setup|intensities: input/input8_zyx.zarr setup|features: ['area', 'area_convex', 'area_filled', 'axis_major_length', 'axis_minor_length', 'bbox', 'centroid', 'eccentricity', 'equivalent_diameter_area', 'euler_number', 'extent', 'inertia_tensor_eigvals', 'moments', 'moments_hu', 'orientation', 'perimeter', 'solidity', 'max_intensity', 'mean_intensity', 'min_intensity'] setup|mode: with-intensities |
name: value |
input/input9.zarr input/input8_zyx.zarr value |
| Test-24 |
labels: input/input12.png setup|intensities: input/input3_uint16.tiff setup|features: label setup|mode: with-intensities |
input/input12.png input/input3_uint16.tiff |
|
| Test-25 |
labels: input/input10.zarr setup|features: label setup|mode: without-intensities |
input/input10.zarr |