Tools & Software¶

Everything AIR uses, in one place. The Classroom Track needs only the first two sections; the rest support the advanced Extension & Research stages.

About third-party tools

AIR is brand-agnostic — these are tools that have worked well, not requirements. Some are hosted by other labs and may occasionally be offline; items marked (offline) were unreachable at last check. Our own Virtual Root simulator is hosted alongside AIR specifically so it stays available.

📲 Data collection & growing¶

Tool	What it's for	Used in
AstroCalibration sticker / AstroBotany Spectrum	Known-size, known-colour marker so software can calibrate photos	Stage I onward
AstroBotany Calibration Image Hub	Community database with client-side marker analysis and metadata sidecar editor	Stage I onward
Metadata Sidecar Generator	CLI & CI/CD tools to generate and validate metadata.csv and Frictionless datapackage.json sidecars	Stages IV+
Epicollect5	Collect & share data from a phone, no account needed	Stages II–IV
Hamama kit	Quick, mess-free microgreen growing	Stage III
Microgreen density calculator	Work out ideal seeding density	Stage III
Google Science Journal	Use a phone's sensors to log light, sound, etc.	Stage III

🔬 Image analysis¶

Tool	What it's for	Used in
PlantCV	Plant computer vision: detect the sticker, colour-correct, measure plants & roots	Stages I, III, IV
PlantCV Semi-Automated GUI	Interactive Streamlit app to tune PlantCV color masking, thresholding, and cleanups for counting leaves/fronds	Stages III, IV
ImageJ / Fiji	General scientific image measurement	General
Easy Leaf Area (Android)	Measure leaf area from a photo	Stage III
SmartRoot	Semi-automated root tracing in ImageJ	Stages IV+
RootNav 2.0 / RootNavPortal	Root system architecture from images	Stages IV+
AstroDart	Root growth & gravitropism analysis	Stages IV, VI
SOAPP / web-glyphics	Analysis using the AstroBotany Spectrum sticker	Stage I, III

🧮 Modelling & simulation¶

Tool	What it's for	Used in
Virtual Root ⭐	Our open, interactive auxin-transport simulator (rebuilds SimuPlant)	Stage VII
SimuPlant	Original desktop auxin model (offline — superseded by Virtual Root)	Stage VII
CRootBox / CPlantBox	Root & whole-plant architecture models	Stages VIII–IX
MARSHAL (app)	Root hydraulic architecture	Stage VIII
MECHA / GRANAR	Root cross-section hydraulic properties	Stage VIII
shinyRootBox, archidart, PlaNet-Maize	Interactive root/plant modelling apps	Stages VIII–IX
RootFit	Root growth curve analysis	Stage III, IV
Photosynthesis model	Interactive photosynthesis simulation	Stage IX

🧬 Molecular biology & spaceflight data¶

Tool	What it's for	Used in
Benchling	DNA sequence storage & lab protocols	Stage V
NASA OSDR / GeneLab (training)	Spaceflight omics data & training	Stage X
Associomics	Membrane-based interactome database	Stage XI
ShinyGO	Gene-ontology enrichment analysis	Stage X
NASA Transform to Open Science (TOPS)	Free open-science training & certification	All stages
GRDN.AI	AI companion-planting hypothesis generator	Stage I (guide)

📊 Data analysis & outreach¶

Tool	What it's for	Used in
R / tidyverse + R-Shiny	Statistics, plotting, interactive analysis	Stages III, IV
QuoVidi	Run large-scale biology "treasure hunts"	Stage III
ResearchGate	Ask & discuss research questions	Stage V
Kids in Space encyclopedia	Kid-friendly space-science reference	All stages

For the science behind these tools, see Literature & References. Tool broken or missing? Edit this page or open an issue on GitHub.