Automated Conidial Germination Counter – Fiji macros, ilastik classifier and demo images

This deposit contains an open-source workflow for automated counting of germinated and non-germinated conidia of entomopathogenic fungi (e.g., Beauveria bassiana) from microscopy images. It is the supplementary material of the article "Automated Conidial Germination Counter: An Open‑Source Workflow for Entomopathogenic Fungi Quality Control" (Frontiers in Fungal Biology).

Contents:

• Three Fiji/ImageJ macros: batch preprocessing, manual counting assistant, and fully automated conidial germination counter.

• A pre‑trained ilastik pixel classifier (project file + 5 training images).

• 10 raw demo images for testing.

Requirements:

• Fiji (Fiji Is Just ImageJ)

• ilastik 1.4.0 or newer

Quick start:

1. Open the ilastik project (classifier.ilp) and export probability maps for your images (TIFF, multi‑channel).

2. Run the Batch_Conidial_Germination_Automated_Counter.ijm macro in Fiji on the exported maps.

3. Obtain germination percentages and visual audit images (overlaid contours).

The workflow achieves 97% concordance with manual counting, processes each image in ~10 seconds, and performs a full census (3,000–9,000 conidia per sample). All material is released under BSD 2‑Clause license. See the README.txt inside the ZIP for detailed step‑by‑step instructions.