ForamEcoQS

ForamEcoQS is a Windows desktop application for ecological quality assessment based on benthic foraminifera. It targets .NET 6, uses Windows Forms for the graphical interface, and can also run in command-line mode. The software calculates multiple biotic and diversity indices from species-by-sample abundance matrices and assigns Ecological Quality Status (EQS) classes where implemented.

Authors and Affiliations

Department of Pure and Applied Sciences (DiSPeA), University of Urbino Carlo Bo (UniUrb)

• Matteo Mangiagalli (m.mangiagalli@campus.uniurb.it)
• Fabrizio Frontalini (fabrizio.frontalini@uniurb.it)
• Carla Cristallo (c.cristallo1@campus.uniurb.it)

Department of Geosciences, University of Fribourg (UNIFR)

• Fabio Francescangeli (fabio.francescangeli@unifr.ch)

Year: 2026

Overview

ForamEcoQS supports a practical analysis workflow:

• Import abundance matrices from Excel or CSV files;
• Create or edit sample tables directly in the application;
• Clean and normalize sample data;
• Calculate selected indices for each sample;
• Review EQS classifications for supported indices;
• Export tables, plots, and EQS agreement summaries.

Main Features

Data Input and Editing

• Create an empty dataset.
• Open existing datasets from Excel or CSV.
• Save the current dataset to Excel.
• Create spreadsheet templates from reference lists.
• Add, remove, and rename sample columns.
• Undo recent data edits.
• Clean and normalize sample values.

Index Calculation

• Compute selected indices from the Advanced Indices workflow.
• Choose threshold systems and reference options from Index Calculation Settings.
• Apply optional EQR calculations for FSI and exp(H'bc).
• Use selected Foram-AMBI lists for eco-group based indices.

Visualization and Export

• Open plot options for calculated results.
• Open a composite dashboard.
• Load existing index tables for plotting without recalculation.
• Export result tables to Excel.
• Export plots to PNG.

Reference Lists Management

• Foram-AMBI List Manager.
• FSI List Manager.
• Geographic Areas Database.
• User Custom Lists Manager.
• Ecological-group override support for taxa assignments.

EQS Comparison Tools

• EQS summary table.
• Pairwise Cohen's kappa matrix.
• Confusion matrices between indices.
• Kappa heatmap.
• Exportable EQS agreement summary.

CLI Mode

• Run the same calculator in command-line mode by passing arguments at startup.
• Read the first worksheet from an Excel input file.
• Print results to console or export them to Excel.

Calculated Indices

Core Ecological / Biotic Indices

• Foram-AMBI
• Foram-M-AMBI
• FSI
• TSI-Med
• NQIf
• FIEI
• BENTIX
• BQI
• FoRAM Index

Diversity / Structure Metrics

• exp(H'bc)
• H'log2
• H'ln
• Simpson (1-D)
• Pielou's J
• ES100

Supporting Metrics

• Species Richness (S)
• Total Abundance (N)
• Ecological group percentages (EG1-EG5)
• FoRAM functional group percentages

Key Thresholds and Criteria Used by the Software

Foram-AMBI EQS Threshold Systems

The threshold system is selectable in Index Calculation Settings.

System	High	Good	Moderate	Poor	Bad
Borja 2003	<= 1.2	<= 3.3	<= 4.3	<= 5.5	> 5.5
Parent 2021	< 1.4	< 2.4	< 3.4	< 4.4	>= 4.4
Bouchet 2025 (Brazilian transitional waters)	< 1.4	< 1.8	< 3.0	<= 4.0	> 4.0

TSI-Med Criteria

Implemented formula:

TSI-Med = ((%TS - %TSref) / (100 - %TSref)) x 100

%TSref is derived from mud percentage (%mud) using the selected reference curve:

• Barras 2014: %TSref = 5.0 + 0.3 x %mud
• Parent 2021 (>125 µm): %TSref = 4.5 + 0.28 x %mud
• Jorissen 2018 homogenized: %TSref = 3.6718 + 0.3247 x %mud

Supported EQS conventions:

Convention	High	Good	Moderate	Poor	Bad
Parent 2021	<= 4	<= 16	<= 36	<= 64	> 64
Barras & Jorissen 2011	> 64	<= 64	<= 36	<= 16	<= 4

The second convention inverts the ecological meaning of low TSI values.

FSI EQS

Class	Rule
High	>= 9
Good	>= 5.5
Moderate	>= 2
Poor	>= 1
Bad	< 1

0 is treated as Azoic.

NQIf EQS

Class	Rule
High	>= 0.54
Good	>= 0.45
Moderate	>= 0.31
Poor	>= 0.13
Bad	< 0.13

exp(H'bc) Threshold Sets

Threshold Set	High	Good	Moderate	Poor	Bad
O'Brien 2021 Norway >125 µm	>= 10	>= 7	>= 5	> 2	<= 2
O'Brien 2021 Norway >63 µm	>= 22	>= 13	>= 7	> 3	<= 3
O'Brien 2021 Italy >63 µm	>= 5	>= 4	>= 3	> 2	<= 2

EQR Logic

Optional EQR mode is available for FSI and exp(H'bc).

• EQR = Observed / Reference
• The value is clamped to the 0.0-1.0 range.

EQS boundaries from EQR:

Class	Rule
High	>= 0.8
Good	>= 0.6
Moderate	>= 0.4
Poor	>= 0.2
Bad	< 0.2

Default reference values exposed by the settings dialog:

• FSI reference value: 10.0
• exp(H'bc) reference value: 20.0

Other Implemented EQS Classifications

Index	High	Good	Moderate	Poor	Bad
BENTIX	>= 4.5	>= 3.5	>= 2.5	>= 2.0	< 2.0
BQI	>= 12	>= 8	>= 5	>= 2	< 2
Foram-M-AMBI	>= 0.81	>= 0.61	>= 0.41	>= 0.21	< 0.21

For BENTIX and BQI, 0 is treated as Azoic.

FoRAM Index Interpretation

Implemented formula:

FI = (10 x Ps) + Po + (2 x Ph)

Where:

• Ps = symbiont-bearing proportion
• Po = stress-tolerant proportion
• Ph = heterotrophic proportion

Interpretation:

• > 4: suitable for coral growth
• 2-4: marginal conditions
• < 2: unsuitable for coral growth

Requirements

• .NET 6 SDK for build and run from source.
• Windows for normal GUI execution.
• A Windows-capable environment for the net6.0-windows target.
• Bundled reference .csv and .xls files available at runtime.

NuGet packages used by the project:

• ClosedXML
• ExcelDataReader
• ExcelDataReader.DataSet
• OxyPlot.Core
• OxyPlot.WindowsForms
• System.Data.DataSetExtensions

Important build note:

• The project targets net6.0-windows.
• On non-Windows systems, dotnet build can fail with NETSDK1100 unless Windows targeting is enabled explicitly.

Build

Standard build:

dotnet restore ForamEcoQS.sln
dotnet build ForamEcoQS.sln -c Release

On non-Windows systems:

dotnet build ForamEcoQS.sln -c Release -p:EnableWindowsTargeting=true

This can build the Windows-targeted application, but GUI execution is still intended for Windows.

Run

Run the GUI

dotnet run --project ForamEcoQS

If no command-line arguments are passed, the application starts in GUI mode, shows the splash screen, and then opens the main window.

Run the CLI

dotnet run --project ForamEcoQS -- -i INPUT_FILE [options]

Supported options:

• -i INPUT_FILE
• -index=INDEX_LIST
• -list LIST_NAME
• -o OUTPUT_FILE
• -mud=VALUE
• -help
• --help
• /?

Supported reference list names for -list:

• jorissen
• alve
• bouchetmed
• bouchetatl
• bouchetsouthatl
• OMalley2021

Accepted index names in -index=:

• exp(H'bc)
• H'log2
• H'ln
• FSI
• TSI-Med
• NQIf
• FIEI
• Foram-AMBI
• Foram-M-AMBI
• BENTIX
• BQI
• FoRAM Index
• Species Richness (S)
• Total Abundance (N)
• Simpson (1-D)
• Pielou's J
• ES100

Example:

dotnet run --project ForamEcoQS -- -i data.xlsx -index=all -list jorissen -o results.xlsx -mud=50

Input File Format

The expected input layout is a species-by-sample matrix:

• The first column must contain species names;
• Each following column represents one sample;
• Positive numeric values are treated as abundances.

CLI mode supports Excel .xls and .xlsx files and reads the first worksheet. GUI mode also supports CSV import.

Output and Exports

ForamEcoQS can produce:

• Calculated result tables in the Advanced Indices window;
• An EQS summary table;
• Excel exports of results;
• PNG exports for generated plots;
• Exports for EQS agreement outputs, including the kappa matrix.

Tools and Databanks

The application includes:

• Selectable Foram-AMBI reference lists;
• A Foram-AMBI List Manager;
• An FSI List Manager;
• A Geographic Areas Database;
• A User Custom Lists Manager;
• Taxon-specific ecological-group overrides;
• Template generation from lists.

Notes and Limitations

• The GUI is Windows-oriented because the project is a Windows Forms application.
• Some indices depend on the selected databank and species classification coverage.
• TSI-Med depends on mud percentage and the selected reference curve.
• FoRAM Index is mainly meaningful for tropical or subtropical reef settings.
• Azoic is treated separately from Bad in several EQS outputs.

References

• Borja A. et al. (2003). AMBI classification boundaries.
• Parent B. et al. (2021). Foram-AMBI and TSI-related threshold updates.
• Bouchet V.M.P. et al. (2025). Brazilian transitional waters Foram-AMBI thresholds.
• Barras C. et al. (2014). TSI-Med reference relationship.
• Jorissen F.J. et al. (2018). Foram-AMBI Mediterranean development.
• O'Brien B.J. et al. (2021). exp(H'bc) thresholds and related foraminiferal EQS work.
• Dimiza M.D. et al. (2016). Foram Stress Index.
• Alve E. et al. (2019). Norwegian Quality Index for foraminifera.
• Simboura N. and Zenetos A. (2002). BENTIX.
• Rosenberg R. et al. (2004). BQI framework.
• Muxika I. et al. (2007). M-AMBI / multivariate ecological quality approach.
• Hallock P. et al. (2003). Original FoRAM Index.
• Prazeres M. et al. (2020). FoRAM Index revisit.
• Mojtahid M. et al. (2006). FIEI.