12,315 Images
ESD Analysis
Carbon Biomass
Optical Properties
Ocean Biology
Species dataset · ESD & morphological parameters · carbon biomass (Menden-Deuer & Lessard 2000) · optical & fluorescence properties · feature histograms from real FlowCAM data · long chain finder for bloom dynamics research.
02
Training Dataset
Class distribution across 2 merged library sources · 10,473 training images
Class Distribution — Library 1 (val split · 2,095 samples)
Balance Ratio
110× imbalance
Sqrt sampling
Stratified split
Multi-Library
Library 110,473 img · 8 classes
Library 21,842 img · 5 classes
Combined12,315 images
Extra classesPennate Diatoms · Richelia
Train/Val Split
Train8,378 (80%)
Validation2,095 (20%)
StrategyStratified
Steps/epoch262
Batch size32
Augmentation Pipeline
RandomFlip horizontal
RandomRotation ±10°
RandomZoom ±10%
RandomTranslation ±6%
No contrast aug ← microscopy
08
ESD & Morphological Parameters
Equivalent Spherical Diameter · biovolume · carbon · aspect ratio · all from FlowCAM CSV columns
Derivation Formulas — based on Menden-Deuer & Lessard 2000
ESD (Diameter)
D_ESD = √(4A/π)
FlowCAM column: "Diameter (ESD)" · units: µm
Biovolume
V = (π/6) × ESD³
Sphere approximation · FlowCAM: "Volume (ESD)" · µm³
Carbon Content
C = 0.109 × V^0.991
Menden-Deuer & Lessard 2000 · units: pgC/cell
Size Class
<2 · 2–20 · >20 µm
Pico · Nano · Micro phytoplankton size classes
ESD · Diameter
6.77 µm
Mean across 12,838 particles
Median bin0–10 µm
Dominant (<10µm)86.9%
Range0 – 110+ µm
FlowCAM: "Diameter (ESD)"
Biovolume
162 µm³
Mean cell biovolume (sphere)
Prochlorococcus0.12 µm³
Nitzschia5,915 µm³
Formulaπ/6 × ESD³
FlowCAM: "Volume (ESD)"
Carbon Content
17.0 pgC
Mean carbon per cell
Prochlorococcus0.015 pgC
Nitzschia~560 pgC
Formula0.109 × V^0.991
Menden-Deuer & Lessard 2000
Aspect Ratio
0.65 mean
Population-weighted mean AR
Most common0.5–0.65
Circular (=1.0)Crocosphaera
Most elongatedNitzschia
FlowCAM: "Aspect Ratio"
ESD Distribution by Species — Literature Values (µm)
Mean ± Std · Menden-Deuer & Lessard 2000 · Chisholm et al. 1992 · Selph et al. 2022
Biovolume vs Carbon Content — Allometric Scaling
C = 0.109 × V^0.991 · pgC/cell vs µm³ per species
Size Class Breakdown — V9 High-Confidence Inference
Pico <2µm · Nano 2–20µm · Micro >20µm · based on 524 high-conf detections
ESD Particle Distribution — Across 19 Cast Stations
% particles in each ESD size bin · 5m vs 10m casts · from FlowCAM CSV
09
Carbon Biomass Estimator
Interactive calculator · Menden-Deuer & Lessard 2000 · pgC/cell from ESD
Interactive Carbon Calculator
36.3
µm³ / cell · Biovolume
4.01
pgC / cell · Carbon
4.01
µgC / mL · Biomass
V = (π/6) × ESD³ · C = 0.109 × V^0.991 · Menden-Deuer & Lessard 2000
Representative Size Classes
Prochlorococcus (Pico, <2 µm)
ESD ~0.6 µm · V ~0.11 µm³ · C ~0.015 pgC/cell
Smallest free-living photosynthetic organism. Dominant in oligotrophic waters.
Synechococcus (Pico, 1–3 µm)
ESD ~1.5 µm · V ~1.77 µm³ · C ~0.21 pgC/cell
Ubiquitous marine picocyanobacterium. Important in nutrient-rich upwelling zones.
Nanophytoplankton (2–20 µm)
ESD ~5–15 µm · V varies · C 1–50 pgC/cell
Major contributors to primary production. Includes flagellates, small diatoms.
Nitzschia (Micro diatom)
ESD ~10–50 µm · High biovolume · C ~100+ pgC/cell
Pennate diatom. Chain-forming. High carbon per cell due to silica frustule.
10
Optical & Fluorescence Properties
RGB channel analysis · scatter · fluorescence channels Ch1/Ch2 · from FlowCAM CSV columns
Color Channel Composition
Key Optical Columns (FlowCAM)
Average Red
Mean pixel intensity R-channel
Average Green
Chlorophyll proxy signal
Average Blue
Scatter / transparency proxy
Ch2/Ch1 Ratio
Fluorescence emission ratio
Scatter Area/Peak
Side scatter · cell size proxy
Optical Classification Significance
Chlorophyll Fluorescence
Green channel (Average Green) and Ch2 correlate with chlorophyll-a content. High values indicate healthy, photosynthetically active cells.
Phycoerythrin
Red fluorescence (Ch1) distinguishes Synechococcus from Prochlorococcus — Synechococcus has phycoerythrin, Prochlorococcus does not.
Side Scatter (SSC)
Scatter Area/Peak captures cell complexity and internal structure. Used to separate mineral particles from biological cells.
Per-Species Optical Fingerprints — Normalized FlowCAM Channels (literature + probe values)
Prochlorococcus · Synechococcus
Nanophyto · Picocyano
Nitzschia · Mineral particles
Radar axes: Red channel · Green channel · Blue channel · Scatter Area · Ch2/Ch1 ratio · Intensity · Values normalized 0–100
13
Feature Histograms
Yeshitha's ESD distribution analysis · BTR-1, BTR-3, BTR-4 · Real FlowCAM data · 12,838 particles · BLOOFINZ-2022 Discrete Casts
BTR-1 — ESD Distribution Analysis
3,130 particles · 2022-03-04
BTR-3 — ESD Distribution Analysis
7,055 particles
BTR-4 — ESD Distribution Analysis
2,653 particles
Source: Yeshitha · Results-Histograms · Discrete-Updated-March 2026 · BLOOFINZ-2022 · ESD (Equivalent Spherical Diameter) Distribution Analysis · Diameter (ABD)
Morphological & Optical Distributions
Computed from BTR-1 + BTR-3 + BTR-4 raw CSV data · 12,838 particles
Cell Size Distribution (ESD µm)
87% in 0–10µm · picoplankton dominant
Fluorescence · Avg Green (chl-a proxy)
Average Green channel · oligotrophic signal
Pixel Intensity (Grayscale)
FlowCAM Intensity column · mean 105.8
Aspect Ratio Distribution
Mean 0.615 · mostly near-spherical
Circularity Distribution
Mean 0.834 · 43% perfectly circular
Elongation Distribution
69% single-cell · diatom long tail
14
Long Chain Finder
Ranked by Particles Per Chain · FlowCAM direct measurement · biological significance for nutrient stress and bloom dynamics
Why Chains Form
Phytoplankton form chains when daughter cells remain attached after division — a response to nutrient limitation (especially Fe, NO₃) or as a competitive strategy in turbulent environments.
Bloom Dynamics
Chain length correlates with growth phase. Longer chains signal rapid division in nutrient-rich waters. Short chains or single cells indicate senescence or nutrient limitation.
FlowCAM "Particles Per Chain"
FlowCAM directly measures chain length during imaging. The column "Particles Per Chain" counts individual cells per chain aggregate — this is the exact biological signal used here.
Search Parameters
⛓
Set parameters and press Find Chains
Particle images load when chain_images.json is pushed from Colab
💡 To enable particle images: Run the chain image export cell in Colab → pushes chain_images.json → images appear automatically
Particles Per Chain · direct FlowCAM measurement
Phytoplankton Classification · Goes Lab (LDEO) · Columbia University · Model v9 · EfficientNetV2-L · TF 2.19
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