DOI: 10.5281/zenodo.4264623
title: Leaf thickness measurements of plants

description: # Analysis Scripts for 'Leveraging Plant Dynamics Using Physical Reservoir Computing' There is leaf thickness and physiological data available from three experiments: a control experiment and two strawberry experiments. In each experiment, the environmental conditions of a growth chamber are modulated (light intensity, temperature and relative humidity) and a single strawberry plant is located inside the chamber. Leaf thickness measurement clips are mounted on the plant except for the control experiment. In this case a plant is still inserted but the clips are not mounted. Physiological data of the plant is collected in all three experiments using a LI6400XT photosynthesis system. An overview of the available parameters is included below. N/A refers to a sensor that is not calibrated and/or temperature compensated. Calibration data is available TODO | parameter | unit | description |<br> |-----------------------------------------------------|-----------|----------------------------------------------------|<br> | light_sensor_lux | lux | light intensity (humain) |<br> | leaf_thickness_1_um | um | thickness of leaf clip 1 |<br> | leaf_thickness_1_nc_au | N/A | thickness of leaf clip 1 |<br> | leaf_temp_1_nc_au | N/A | temperature of leaf clip 1 |<br> | leaf_thickness_2_um | um | thickness of leaf clip 2 |<br> | leaf_thickness_2_nc_au | N/A | thickness of leaf clip 2 |<br> | leaf_temp_2_nc_au | N/A | temperature of leaf clip 2 |<br> | leaf_thickness_3_um | um | thickness of leaf clip 3 |<br> | leaf_thickness_3_nc_au | N/A | thickness of leaf clip 3 |<br> | leaf_temp_3_nc_au | N/A | temperature of leaf clip 3 |<br> | leaf_thickness_4_um | um | thickness of leaf clip 4 |<br> | leaf_thickness_4_nc_au | N/A | thickness of leaf clip 4 |<br> | leaf_temp_4_nc_au | N/A | temperature of leaf clip 4 |<br> | leaf_thickness_5_um | um | thickness of leaf clip 5 |<br> | leaf_thickness_5_nc_au | N/A | thickness of leaf clip 5 |<br> | leaf_temp_5_nc_au | N/A | temperature of leaf clip 5 |<br> | leaf_thickness_6_um | um | thickness of leaf clip 6 |<br> | leaf_thickness_6_nc_au | N/A | thickness of leaf clip 6 |<br> | leaf_temp_6_nc_au | N/A | temperature of leaf clip 6 |<br> | leaf_thickness_7_um | um | thickness of leaf clip 7 |<br> | leaf_thickness_7_nc_au | N/A | raw leaf thickness measurement |<br> | leaf_temp_7_nc_au | N/A | temperature of leaf clip 7 |<br> | leaf_thickness_8_um | um | thickness of leaf clip 8 |<br> | leaf_thickness_8_nc_au | N/A | thickness of leaf clip 8 |<br> | leaf_temp_8_nc_au | N/A | temperature of leaf clip 8 |<br> | ref_mon_0 | N/A | monitor of the 3.3V ADC reference (board 0) |<br> | ref_mon_1 | N/A | monitor of the 3.3V ADC reference (board 1) |<br> | ref_mon_2 | N/A | monitor of the 3.3V ADC reference (board 2) |<br> | ref_mon_3 | N/A | monitor of the 3.3V ADC reference (board 3) |<br> | soil_water_content_nc_au | N/A | soil water concentration |<br> | air_temperature_C | degree C | air temperature |<br> | relative_humidity_percent | % | relative humidity |<br> | li6400xt_external_probe_air_temperature_C | degree C | air temperature of external probe |<br> | li6400xt_external_probe_relative_humidity_percent | % | rel. humidity of external probe |<br> | li6400xt_photosynthetic_rate_umol/m2/s | umol/m2/s | photosynthetic rate |<br> | li6400xt_stomatal_conductance_mol/m2/s | mol/m2/s | stomatal conductance |<br> | li6400xt_transpiration_rate_mmol/m2/s | mmol/m2/s | transoration rate |<br> | li6400xt_vapour_pressure_deficit_kPa | kPa | vapour pressure deficit |<br> | li6400xt_sample_cell_air_temperature_C | degree C | air temperature in the sample cell |<br> | li6400xt_leaf_temperature_C | degree C | temperature of leaf inside sample cell |<br> | li6400xt_ref_cell_CO2_conc_umol/mol | umol/mol | CO2 concentration in the reference cell |<br> | li6400xt_sample_cell_CO2_conc_umol/mol | umol/mol | CO2 concentration in the sample cell |<br> | li6400xt_ref_cell_H2O_conc_mmol/mol | mmol/mol | H2O concentration in the reference cell |<br> | li6400xt_sample_cell_H2O_conc_mmol/mol | mmol/mol | H2O concentration in the sample cell |<br> | li6400xt_ref_cell_relative_humidity_conc_percent | % | Rel. humidity in the reference cell |<br> | li6400xt_sample_cell_relative_humidity_conc_percent | % | Rel. humidity in the sample cell |<br> | li6400xt_PAR_inside_chamber_umol/m2/s | umol/m2/s | PAR inside leaf chamber |<br> | li6400xt_PAR_outside_chamber_umol/m2/s | umol/m2/s | PAR outside leaf chamber |<br> | li6400xt_air_pressure_kPa | kPa | air pressure |<br> | time | time | sample time |<br> | train_val_test_split | | data split on da day-basis, all days equal |<br> | train_val_test_split2 | | data split on da day-basis, train focus on first 5 |<br> | di_2 | | discard interval for +-2h from center of night |<br> | di_4 | | discard interval for +-4h from center of night |<br> | di_6 | | discard interval for +-6h from center of night |<br> | di_9 | | discard interval for +-9h from center of night |<br> | di2_2 | | discard interval for +-2h from center of night |<br> | di2_4 | | discard interval for +-4h from center of night |<br> | di2_6 | | discard interval for +-6h from center of night |<br> | di2_9 | | discard interval for +-9h from center of night | Non-calibrated variables are usually RAW ADC readout values. The ADC range is 0-3.3V, where the midpoint is at 1.65V (0x0). `train_val_test_split` interleaves the train and test splits, such that drift in the system is automatically compensated for, while `train_val_test_split2` does not. The test data is always at the end of the analysis. `train_val_test_split` should be used with `di_`, and `train_val_test_split2` should be used with `di2_`. Three data formats are available: `data`, `full_data` and `mini_data`. `data` was used to generate the results. It is a cropped version of `full_data` that discards part of the start of the experiment and end to remove transient effects at the start. `mini_data` is a subsampled dataset, with sample spacing of 60s (sample interval), which is useful for plotting and fast analysis.