These files will be created in the directory specified with the --outdir parameter
The Shiny app that is automatically launched at the end of a pipeline run. It allows to interactively explore pipeline results.
Note that the shiny app can also be run manually as described here.
The main result of the pipeline. It includes a total of 78 traits.
| file | format | plant_region_red_channel | plant_region_green_channel | plant_region_blue_channel | plant_region_chroma_ratio | plant_region_chroma_difference | plant_region_chroma_base | plant_region_green_strength | plant_region_blue_green_ratio | total_area | class_background_area | plant_region_area | plant_region_filled_area | plant_region_convex_area | plant_region_equivalent_diameter | plant_region_major_axis_length | plant_region_minor_axis_length | plant_region_perimeter | plant_region_eccentricity | plant_region_extent | plant_region_solidity | plant_region_aspect_ratio | class_norm_area | class_norm_filled_area | class_norm_convex_area | class_norm_equivalent_diameter | class_norm_major_axis_length | class_norm_minor_axis_length | class_norm_perimeter | class_norm_eccentricity | class_norm_extent | class_norm_solidity | class_norm_aspect_ratio | class_norm_red_channel | class_norm_green_channel | class_norm_blue_channel | class_norm_chroma_ratio | class_norm_chroma_difference | class_norm_chroma_base | class_norm_green_strength | class_norm_blue_green_ratio | class_senesc_area | class_senesc_filled_area | class_senesc_convex_area | class_senesc_equivalent_diameter | class_senesc_major_axis_length | class_senesc_minor_axis_length | class_senesc_perimeter | class_senesc_eccentricity | class_senesc_extent | class_senesc_solidity | class_senesc_aspect_ratio | class_senesc_red_channel | class_senesc_green_channel | class_senesc_blue_channel | class_senesc_chroma_ratio | class_senesc_chroma_difference | class_senesc_chroma_base | class_senesc_green_strength | class_senesc_blue_green_ratio | class_antho_area | class_antho_filled_area | class_antho_convex_area | class_antho_equivalent_diameter | class_antho_major_axis_length | class_antho_minor_axis_length | class_antho_perimeter | class_antho_eccentricity | class_antho_extent | class_antho_solidity | class_antho_aspect_ratio | class_antho_red_channel | class_antho_green_channel | class_antho_blue_channel | class_antho_chroma_ratio | class_antho_chroma_difference | class_antho_chroma_base | class_antho_green_strength | class_antho_blue_green_ratio |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | png | 99.7535697835099 | 126.85610317825886 | 93.1953707968678 | 1.3149188878330613 | -30.38163288807 | 1.5210063666329467 | 0.39666698713482385 | 0.7346542141997628 | 295872 | 252088 | 43420 | 43420 | 74876 | 235.1256281914006 | 337.28373985034574 | 280.94370163968136 | 2842.266340221731 | 0.5533339317860381 | 0.3790153631284916 | 0.5798920882525775 | 1.2005385345243373 | 43420 | 43420 | 74876 | 235.1256281914006 | 337.28373985034574 | 280.94370163968136 | 2842.266340221731 | 0.5533339317860381 | 0.3790153631284916 | 0.5798920882525775 | 1.2005385345243373 | 99.7535697835099 | 126.85610317825886 | 93.1953707968678 | 1.3149188878330613 | -30.38163288807 | 1.5210063666329467 | 0.39666698713482385 | 0.7346542141997628 | 364 | 364 | 4878 | 21.528102431092233 | 118.79161550599903 | 57.90022379861881 | 108.84062043356593 | 0.8731732196472067 | 0.033734939759036145 | 0.07462074620746208 | 2.051660731384475 | 151.60164835164835 | 146.17582417582418 | 102.5 | 1.1505303104018683 | -19.125 | 1.7383288227334235 | 0.3651862375687195 | 0.7012103443091264 | 0 | 0 | 0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan |
| 2 | png | 101.51583105439076 | 94.147645092677 | 72.06311151625646 | 1.0847818715609308 | -7.3581738073533955 | 1.8436886275783073 | 0.3516559409148823 | 0.7654265961227072 | 295872 | 253178 | 32910 | 33290 | 49295 | 204.70054571796874 | 249.0253277199329 | 226.85573677295378 | 2268.613490585595 | 0.41246255897980133 | 0.5141544806899138 | 0.6676133482097576 | 1.0977255028342852 | 19641 | 20071 | 37765 | 158.13822402614534 | 243.5850984756978 | 192.0965839059821 | 1678.7646814565664 | 0.6148782278468807 | 0.38401830055136277 | 0.5200847345425659 | 1.268034514319712 | 99.8897713965684 | 100.23354208034215 | 69.94267094343465 | 1.180381565492363 | -15.317320910340612 | 1.6943673626127465 | 0.37114463820935434 | 0.6977970596646393 | 9784 | 9784 | 43914 | 111.6126144559334 | 297.684598907779 | 238.1577090039546 | 1840.238815542512 | 0.5999550734143577 | 0.17297526651698106 | 0.2227991073461766 | 1.2499473569542774 | 181.04732215862632 | 147.45860588716272 | 118.13000817661488 | 0.9857605569374454 | 2.1300592804578855 | 2.028890267443432 | 0.33015392163548435 | 0.8011062322602557 | 13269 | 13269 | 40074 | 129.97928880822082 | 263.4953771674782 | 218.30785211698048 | 1249.9341622907673 | 0.5599782135538464 | 0.20730221222347206 | 0.3311124419823327 | 1.2069899209410202 | 103.92275227974979 | 85.1391966237094 | 75.2018237998342 | 0.9506143544019616 | 4.423091416082599 | 2.1039025875621395 | 0.322175059232583 | 0.8832808715849704 |
| 3 | png | 108.62245148181881 | 64.93773208155258 | 85.61668885307924 | 0.6686369386683856 | 32.181838085896445 | 2.9911599020883766 | 0.2505537298760567 | 1.318442854541899 | 295872 | 231465 | 57092 | 59107 | 66287 | 269.61415409436484 | 282.5393177149983 | 275.3537751428984 | 2252.772870152029 | 0.22409201595728792 | 0.6452094116583414 | 0.8612850181785268 | 1.0260956748036987 | 1916 | 1916 | 2629 | 49.391567779455755 | 84.53543546012013 | 39.44852380148291 | 288.492424049175 | 0.8844416790722189 | 0.4344671201814059 | 0.7287942183339673 | 2.142930262372514 | 54.258872651356995 | 43.45198329853862 | 38.906054279749476 | 0.9327970241563215 | 3.1304801670146105 | 2.1440891728925937 | 0.3180571367446267 | 0.89538040214284 | 7315 | 7315 | 74192 | 96.50775756247637 | 446.15984262710236 | 368.77434463230827 | 1426.7747827243331 | 0.562860252529645 | 0.07713071626651483 | 0.09859553590683631 | 1.2098451237760381 | 214.53465481886533 | 149.2384142173616 | 167.21435406698563 | 0.7818666754521229 | 41.63609022556389 | 2.5579808716664876 | 0.2810582844790899 | 1.1204511582617234 | 55176 | 59107 | 66287 | 265.05143863089546 | 287.15623600302183 | 279.6677112463133 | 2383.412480458819 | 0.22688405626546063 | 0.6235562687882829 | 0.8323804064145307 | 1.0267765081758513 | 110.51023995940264 | 65.68382992605481 | 87.23872698274612 | 0.6643152775131367 | 33.19065354501956 | 3.0106187042498815 | 0.2493380881459368 | 1.3281613919431503 |
| 4 | png | 111.70213353269308 | 54.769555466099256 | 69.44015182011617 | 0.6047130890440635 | 35.80158721030538 | 3.3073535801277596 | 0.2321611127104962 | 1.267860424083551 | 295872 | 179415 | 86945 | 88760 | 137905 | 332.7188185495355 | 420.9388337170134 | 375.5729285951652 | 5858.3327163372105 | 0.4515874805735622 | 0.44814700273181796 | 0.6304702512599253 | 1.1207912010366132 | 4618 | 4618 | 11644 | 76.6799857693452 | 129.0989850974666 | 86.86193146231405 | 688.4467888754755 | 0.7397952873883376 | 0.284604955010477 | 0.3965991068361388 | 1.4862550593118866 | 46.969034213945434 | 37.82459939367692 | 33.35708098744045 | 0.9417758919087955 | 2.338458207016018 | 2.1236474804492937 | 0.3201385579707489 | 0.8818885466640712 | 29512 | 29514 | 221347 | 193.84490048547607 | 697.0170486153787 | 573.5354717863108 | 3107.4328624631016 | 0.5682690370730274 | 0.10330511975020827 | 0.13332911672622624 | 1.2152989359916608 | 228.63516535646517 | 183.52012740580102 | 169.83809975603145 | 0.9211163883428404 | 15.71650515044729 | 2.171278272008768 | 0.3153302593551888 | 0.9254467188794188 | 82327 | 84145 | 137905 | 323.7622460995286 | 430.53517634575854 | 385.094631093112 | 6084.392636860784 | 0.44715662610668927 | 0.42434410597391886 | 0.59698343062253 | 1.117998386847568 | 115.3332321109721 | 55.72005538887607 | 71.46417335746474 | 0.5965827549814773 | 37.67864734534236 | 3.3524267728156105 | 0.2297568809763327 | 1.2825574716088999 |
| 5 | png | 73.44000517196794 | 97.80629132956518 | 62.51501717832207 | 1.4388036519543341 | -29.828780154420187 | 1.3900437334054512 | 0.41840238570662097 | 0.6391717376101432 | 295872 | 241734 | 54138 | 54216 | 90528 | 262.5464577420008 | 340.861057612292 | 332.22817379633966 | 3066.5638507985386 | 0.22363351094797934 | 0.42607545922463047 | 0.5980249204665959 | 1.0259848035080985 | 54138 | 54216 | 90528 | 262.5464577420008 | 340.861057612292 | 332.22817379633966 | 3066.5638507985386 | 0.22363351094797934 | 0.42607545922463047 | 0.5980249204665959 | 1.0259848035080985 | 73.44000517196794 | 97.80629132956518 | 62.51501717832207 | 1.4388036519543341 | -29.828780154420187 | 1.3900437334054512 | 0.41840238570662097 | 0.6391717376101432 | 0 | 0 | 0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | 0 | 0 | 0 | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan | nan |
| 6 | png | 110.51932698278792 | 62.721208712667114 | 79.72029479653649 | 0.6593916464512628 | 32.39860217699509 | 3.0330987824363116 | 0.24794830326370548 | 1.2710261239024283 | 295872 | 199546 | 85347 | 88796 | 134622 | 329.6470467401641 | 386.5541628985788 | 368.2250540537557 | 4409.001584426775 | 0.30427781368429097 | 0.45090342349957735 | 0.6339751303650221 | 1.0497769194220752 | 4149 | 4149 | 5231 | 72.68198450170571 | 113.65867058658988 | 59.35338059729336 | 368.19090885900994 | 0.852818620312283 | 0.490715552927262 | 0.7931561842859873 | 1.9149485579895167 | 53.84646902868161 | 48.90961677512654 | 42.10122921185828 | 1.0195057864235706 | -0.9357676548565905 | 1.961734819589407 | 0.3376399512156975 | 0.8607965465243488 | 10979 | 10979 | 109781 | 118.23238541807127 | 565.4087715222331 | 318.9288386884033 | 1129.6082604829626 | 0.8257285287115241 | 0.07754188208040229 | 0.10000819813993314 | 1.7728367677488182 | 219.75799253119592 | 163.97395026869478 | 141.17752072137716 | 0.9086052452475086 | 16.49380635759175 | 2.201175934720903 | 0.3123852048098024 | 0.860975298149722 | 81198 | 81993 | 134622 | 321.5346086401987 | 395.7318516118371 | 376.875437230469 | 4490.729506488133 | 0.30500569617415274 | 0.42898351648351646 | 0.6031555020724696 | 1.0500335456190448 | 113.41515800881795 | 63.42694401339934 | 81.64252814108723 | 0.6503403712546313 | 34.10189906155325 | 3.0753126953223227 | 0.24537994376426825 | 1.2871900012057924 |
Traits are calculated per class and within the plant region that, by default, includes all classes except senescence.
Note that this is controlled by the
--ignore_senescenceparameter.
These traits are based on the color channel information of the original plant images within the region of the segmented mask. Color indices are calculated as described in Del Valle et al. 2018.
Mean of {red|green|blue} channel intensities within the mask region of the original image.
These traits are calculated for each classified region using scikit-image. Please refer to the relevant sections of the scikit-image documentation for further information.
Number of pixels of the region.
Number of pixels of the region will all the holes filled in.
Number of pixels of convex hull image, which is the smallest convex polygon that encloses the region.
The diameter of a circle with the same area as the region.
The length of the major axis of the ellipse that has the same normalized second central moments as the region.
The length of the minor axis of the ellipse that has the same normalized second central moments as the region.
The aspect ratio of the ellipse enclosing the region.
Ratio of pixels in the region to pixels of the convex hull image.
Eccentricity of the ellipse that has the same second-moments as the region. The eccentricity is the ratio of the focal distance (distance between focal points) over the major axis length. The value is in the interval [0, 1]. When it is 0, the ellipse becomes a circle.
Ratio of pixels in the region to pixels in the total bounding box.
Perimeter of object which approximates the contour as a line through the centers of border pixels using a 4-connectivity.
This folder contains diagnostic images for each processed input image.
Note that the
--ignore_senescenceparameter controls whether senescent leaves are included in the calculation of the convex hull.
This folder contains diagnostic images summarised for each chunk of processed images (number of images is controlled by the --chunksize parameter)
Note that the creation of these files depends on the
--summary_diagnosticsparameter that is set tofalseby default.
This folder contains reports that are generated by Nextflow.