Time-lapse images of Arabidopsis thaliana photoreceptor mutants under darkness and blue-light conditions

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 ..., 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 collec..., , ## 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...