DOI: 10.5061/dryad.9kd51c5t0
title: Time-lapse images of Arabidopsis thaliana photoreceptor mutants under darkness and blue-light conditions

description: Rapid cell expansion pushes the Arabidopsis hypocotyl (juvenile stem)
 through the soil until blue light acting first through phototropin 1
 (phot1) and then through cryptochrome 1 (cry1) suppresses elongation to
 produce the short hypocotyl characteristic of established,
 photosynthetically capable seedlings. To determine where these two
 different blue light receptors act to suppress hypocotyl elongation, we
 measured relative elemental growth rate specifically along the hypocotyl
 midline at 5-minute intervals before and during blue light using a machine
 learning-based image analysis pipeline designed specifically for this
 kinematic analysis of growth. In darkness, hypocotyl material expanded
 most rapidly (approximately 4% h⁻¹) in a zone from 0.4 to 1.5 mm below the
 apical terminus of the hypocotyl (cotyledonary node). Blue light
 acting through phot1 rapidly inhibited expansion in this zone, while
 simultaneously stimulating unexpanded cells in a more apical region only
 0.1–0.3 mm below the cotyledonary node. Nuclear cry1, and not its
 cytoplasmic pool, counteracted the phot1-initiated expansion of the small
 cells in this apical region, preventing them from entering the more basal
 elongation zone. In a cry1 mutant, activation of these apical
 cells proceeded unchecked, reaching rates as high as 6% h⁻¹ to produce the
 iconic cry1 long-hypocotyl phenotype. In addition to showing where future
 cell and molecular studies of cry1 and phot1 signaling mechanisms should
 focus, the new spatial information indicates that a seedling may use an
 apical reservoir of elongation potential to reenter a lit environment
 should a natural darkening event such as soil disturbance deactivate
 cry1. 
description: A clear plastic Petri plate with seedlings growing vertically on
 the surface of agar was mounted perpendicular to the optical axis of a
 macro video zoom lens (18–108 mm f/2.5, Edmund Optics)
 fitted to a charge-coupled device camera (Marlin F-146B; Allied Vision)
 that was controlled by a computer. A close-up +4 lens (Tiffen) attached to the
 zoom lens increased magnification. An infrared-pass
 filter (R72, Hoya
 Filter USA) permitted 948 nm infrared radiation emitted by a
 BL020201 backlight (Advanced
 Illumination) placed behind the seedlings to reach the camera,
 which was made sensitive to infrared by removal of the internal
 infrared-blocking filter. This platform produced images of growing
 seedlings at a resolution of 184 px mm⁻¹, even in the complete absence of
 visible light. This arrangement ensured that blue light produced by an LED
 source described in Wu and Spalding treated the seedlings with a fluence rate of approximately 80 μmol m⁻² s⁻¹ without affecting the image the camera collected. All experiments were performed in a photobiology darkroom. Some manipulations required brief use of a dim green safelight.  The camera collected images every 5 minutes. The indicated light treatment began at frame 24, 2 hours after the start of recording in complete darkness. Image collection continued every 5 minutes for 8 hours. The 96 images per trial were stored in Tagged Image File Format (TIFF). These time series of images were used to develop the analysis pipeline, and they were the raw experimental data used to characterize the kinematics of light responses in the wild type and the indicated mutant genotypes.
description: ## HypoQuantyl Image Datasets Sample image datasets to test
 HypoQuantyl's image processing and analysis pipeline. This data
 repository contains files used for the image analysis software
 [HypoQuantyl](https://github.com/jbustamante35/hypoquantyl). Included here
 are sample time-lapse images of *Arabidopsis thaliana* seedlings for users
 to test out the pipeline. Instructions for installing and running the
 software are detailed in the GitHub repository's README file. ###
 Files and Variables #### File: `multiple_seedling.zip` **Description:**
 Time-lapse imaging of five wild-type *Arabidopsis thaliana* seedlings
 grown for 6 hours under blue light after 2 hours in darkness. #### File:
 `single_seedling.zip` **Description:** Time-lapse imaging of a single
 *cry1* mutant *Arabidopsis thaliana* seedling grown for 8 hours in
 darkness. #### File: `HQ.mat` **Description:** MATLAB dataset containing
 trained neural network models, PCA means and eigenvectors, and various
 functions and constants necessary for the HypoQuantyl analysis pipeline to
 run properly. #### Variables * `HQ.models`: neural network models *
 `HQ.pca`: PCA eigenvectors and means * `HQ.functions`: helper functions
 for the analysis pipeline * `HQ.constants`: constants and other values
 used by the pipeline