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Output directory structure

These files will be created in the directory specified with the --outdir parameter

Shiny app

The Shiny app that is automatically launched at the end of a pipeline run. It allows to interactively explore pipeline results.

Shiny screenshot

Note that the shiny app can also be run manually as described here.

Trait table

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_senescence parameter.

Color channel quantification

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.

{class_norm|class_senesc|class_antho|plant_region}_{red|green|blue}_channel

Mean of {red|green|blue} channel intensities within the mask region of the original image.

{class_norm|class_senesc|class_antho|plant_region}_chroma_base

Chroma base

{class_norm|class_senesc|class_antho|plant_region}_chroma_ratio

Chroma ratio

{class_norm|class_senesc|class_antho|plant_region}_chroma_difference

Chroma difference

{class_norm|class_senesc|class_antho|plant_region}_green_strength

Strength of Green

{class_norm|class_senesc|class_antho|plant_region}_blue_green_ratio

Blue Green ratio

Morphometric traits

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.

{class_norm|class_senesc|class_antho|plant_region}_area

Number of pixels of the region.

{class_norm|class_senesc|class_antho|plant_region}_filled_area

Number of pixels of the region will all the holes filled in.

{class_norm|class_senesc|class_antho|plant_region}_convex_area

Number of pixels of convex hull image, which is the smallest convex polygon that encloses the region.

{class_norm|class_senesc|class_antho|plant_region}_equivalent_diameter

The diameter of a circle with the same area as the region.

{class_norm|class_senesc|class_antho|plant_region}_major_axis_length

The length of the major axis of the ellipse that has the same normalized second central moments as the region.

{class_norm|class_senesc|class_antho|plant_region}_minor_axis_length

The length of the minor axis of the ellipse that has the same normalized second central moments as the region.

{class_norm|class_senesc|class_antho|plant_region}_aspect_ratio

The aspect ratio of the ellipse enclosing the region.

{class_norm|class_senesc|class_antho|plant_region}_solidity

Ratio of pixels in the region to pixels of the convex hull image.

{class_norm|class_senesc|class_antho|plant_region}_eccentricity

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.

{class_norm|class_senesc|class_antho|plant_region}_extent

Ratio of pixels in the region to pixels in the total bounding box.

{class_norm|class_senesc|class_antho|plant_region}_perimeter

Perimeter of object which approximates the contour as a line through the centers of border pixels using a 4-connectivity.

Diagnostics

This folder contains diagnostic images for each processed input image.

Convex Hull

Hull example

Note that the --ignore_senescence parameter controls whether senescent leaves are included in the calculation of the convex hull.

Crop

Crop example

Mask

Mask example

Overlay

Overlay example

Summary

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_diagnostics parameter that is set to false by default.

Summary Crop

Crop example

Summary Mask

Crop example

Summary Overlay

Crop example

www

This folder contains reports that are generated by Nextflow.