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Additional file 5: Figure S5. Validation of the screening method by interfering with auxins. Per treatment, 1 µM of NAA, 2,4-D, IAA, and NPA was added. The shoot parameters are the lengths (in mm) of the total shoot, internode, coleoptile, and leaves 1 and 2. The root parameters are the lengths (in mm) of the seminal and crown roots and the number of emerged crown roots. Different letters indicate statistically significant differences between treatments (see “Methods”). The root data for the 2,4-D treatment are not available, because the root system was unmeasurable. The picture shows the harvested rice seedling treated with 1 µM 2,4-D with the “stumpy” root phenotype. Scale bar, 1 cm.

Additional file 15. Python source code used to make Plength.

Additional file 4: Figure S4. Graphical User Interface of Plength and its interference functionalities. Top panel: GUI with an uploaded image. Information on the file directory and image size are displayed. Bottom panel: Interference functionalities. (A) The four settings that can be changed, i.e. plant type, coleoptile or seedling, scale bar position and length, and minimum detection area. (B) Preprocessing. Before the analysis, the image can be cropped and the detected areas can be checked. (top) cropping tool; (bottom) color thresholding tool. (C) Postprocessing. The display after analysis completion. Detected regions are framed and numbered and the leaves are traced. For each detected area, the shoot, internode and leaf lengths are given.

Additional file 6: Figure S6. Validation of the screening method by interfering with cytokinins. Per treatment, 1 µM of kinetin, 2iP, and trans-zeatin was added. The shoot parameters are the lengths (in mm) of the total shoot, internode, coleoptile, and leaves 1 and 2. The root parameters are the lengths (in mm) of the seminal and crown roots and the number of emerged crown roots. Different letters indicate statistically significant differences between treatments (see “Methods”).

Additional file 3: Figure S3. Theoretical example of the analysis of artificial plants with three or four leaves. Detected regions are numbered and framed. Leaves are traced in yellow.

Additional file 8: Figure S8. Validation of the screening method by interference with the ethylene pathway. Per treatment, 1 µM of ACC and AgNO3 was added. The shoot parameters are the lengths (in mm) of the total shoot, internode, coleoptile, and leaves 1 and 2. The root parameters are the lengths (in mm) of the seminal and crown roots and the number of emerged crown roots. Different letters indicate statistically significant differences between treatments (see “Methods”).

Additional file 2: Figure S2. Extra information about the image processing pipeline in Plength. Top panel: Smoothing improving thresholding by homogenizing the colors, removal of the noise, and connection of edges. Middle panel: Segmentation, i.e. thresholding and partitioning of the image into individual plants. Bottom panel: Prior to feature extraction, skeletonization of the contour, conversion to a graph, and pruning. The red and green dots indicate nodes and connecting edges, respectively. Note that the initial graph consists of nine nodes, but the pruned graph of only of seven.

Additional file 9: Figure S9. Validation of the screening method by means of a concentration range of NaCl in Oryza sativa (L.) cv. Chucheongbyeo. Also 1 µM GA3 was added in the test tubes. Mock_DMSO corresponds to GA3 as this is also dissolved in DMSO, while NaCl is dissolved in sterile dH2O. The shoot parameters (in mm) are lengths of total shoot, internode, coleoptile, and leaves 1 and 2. The root parameters are lengths (in mm) of the seminal and crown roots and the number of emerged crown roots. Different letters indicate statistically significant differences between the treatments (see “Methods”).