Digital Microscopy and Automated Spore Analysis
Calibrated image capture, measurement and machine-assisted analysis of spores and microscopic structures for taxonomy and aerobiology.
Program identification
- 1.1Program name
- Digital Microscopy and Automated Spore Analysis
- 1.2Type of qualification
- Course
- 1.3Provider / endorsing institution
- Fungaris – International Institute of Mycology, School of Digital Mycology: AI, Genomics & Data. A Fungaris program of its own, not endorsed by a university.
- 1.4Mode of study
- Online, with live sessions in a small group, recordings and a virtual campus.
- 1.5Duration (hours / ECTS credits)
- 3 months (12 weeks) · 72 hours in total · 6 modules of 12 hours · 12 live sessions of 2 hours. ECTS credits: not applicable (Fungaris own program, not an official university degree).
- 1.6Language
- English
- 1.7Start and end dates / intake
- Next intake: January 11, 2027 to April 2, 2027. Enrollment closes on January 4, 2027. Following intake: March 8, 2027. How intakes work →
Overview
2.1Program description
Digital Microscopy and Automated Spore Analysis teaches you to capture, measure and analyze microscopic fungal structures in a consistent, reproducible way. You choose and calibrate microscope cameras, follow image capture standards that make photos useful to others, and measure spores accurately in ImageJ/Fiji. Later modules move into segmentation, automated counting and deep learning models that classify spores, and finish with sound practices for sharing and archiving image data.
Spore dimensions and ornamentation are central to fungal taxonomy, while spore counts matter in aerobiology and allergy monitoring. Manual measurement is slow and inconsistent, and automated tools are maturing quickly. The course suits microscopists, taxonomists and aerobiologists who want reliable digital workflows. For the final project you build a calibrated image set for a group of species or a spore trap sample, measure or count spores with a semi-automated pipeline and document the workflow so others can reproduce it.
2.2Why it matters / what need it meets
It meets a practical need: applied, up-to-date knowledge in digital mycology, useful in areas such as taxonomy and collections, aerobiology and air quality, plant pathology, food and building diagnostics.
Mycology is moving fast and good practical training is still scarce. This program gives you a structured path, taught live by people who work in the field, so you can apply what you learn with judgment and safety.
Objectives and competences
3.1General objective
To finish the program able to apply its content professionally and with judgment. In short:
Calibrated image capture, measurement and machine-assisted analysis of spores and microscopic structures for taxonomy and aerobiology.
3.2Specific objectives
- Build the foundations: Microscope cameras and calibration; Image capture standards for fungi.
- Put them into practice: Measuring spores with ImageJ/Fiji; Segmentation and automated counting.
- Apply everything to a real case: Deep learning for spore classification; Sharing and archiving image data.
- Complete a final project reviewed by your instructor.
3.3Competences you will gain
- Calibrate microscope cameras and capture standardized fungal images.
- Measure spores accurately and summarize dimensions statistically in Fiji.
- Segment and count spores automatically from slide images.
- Train and evaluate a simple deep learning spore classifier.
- Archive and share microscopy images with complete metadata.
Student profile
4.1Who it is for (entry profile)
Microscopists, taxonomists and aerobiologists.
4.2Entry requirements
Basic experience with a light microscope is recommended; a microscope camera is helpful but sample images are provided.
4.3Career paths (exit profile)
- Microscopy technician in a herbarium or research lab
- Taxonomist using digital measurement workflows
- Aerobiology analyst in a pollen and spore monitoring network
- Image analysis specialist in plant pathology
- Quality control microscopist in food or indoor air testing
Outcomes depend on your experience and on your local market.
Study plan
5.1Overall structure (modules and workload)
| Module | Title | Phase | Topics | Hours |
|---|---|---|---|---|
| 01 | Microscope cameras and calibration | Foundations | 3 | 12 |
| 02 | Image capture standards for fungi | Foundations | 3 | 12 |
| 03 | Measuring spores with ImageJ/Fiji | Practice | 3 | 12 |
| 04 | Segmentation and automated counting | Practice | 3 | 12 |
| 05 | Deep learning for spore classification | Application & project | 3 | 12 |
| 06 | Sharing and archiving image data | Application & project | 3 | 12 |
| Total | 72 |
6 modules × 12 hours = 72 hours: 24 hours of live sessions, and the rest for campus study, exercises and the final project.
5.2Content by module
Hover or tap a module to follow the path from the first session to the final project. Open a module to see the topics it covers.
- Choosing a microscope camera
- Calibrating with a stage micrometer
- Lighting, contrast and white balance
- Mounting media and stains
- Focus stacking and resolution
- Metadata to record with every image
- Setting scale in Fiji
- Measuring length, width and Q values
- Statistics of spore measurements
- Thresholding and segmentation
- Separating touching objects
- Counting spores on trap slides
- Building labeled spore datasets
- Training a classification model
- Evaluating and improving accuracy
- File formats and image repositories
- Licenses and attribution
- Linking images to specimens
5.3Company placement
This program does not include a company placement. Practice is built into every module through exercises, case studies and the final project.
5.4Final project
A calibrated, documented image set with semi-automated spore measurements or counts for a chosen group or trap sample.
Methodology
6.1How it is taught
- Live online sessions, usually weekly, with a working professional and a small group.
- Recordings of every session, so you can catch up if work or time zones get in the way.
- Exercises and real case studies in every module.
- Tutoring: your instructor answers questions and gives feedback on your exercises and project.
6.2Platform and resources
A Moodle virtual campus with session recordings, readings, exercises and forums for each module. You need a computer, an up-to-date browser and a stable connection; a webcam and microphone are recommended.
Technical requirements →6.3Estimated weekly workload
About 6 hours a week for 12 weeks: one 2-hour live session on a weekday evening, plus study and exercises on the campus at your own pace.
Assessment
7.1Assessment system and weighting
Progress is assessed through participation in live sessions, image analysis exercises in each module and a final project reviewed by the instructor.
7.2Requirements to pass
- Complete every module, by attending the live sessions or watching the recordings.
- Hand in the module exercises.
- Have your final project approved by your instructor.
Teaching team
8.1Academic direction
At Fungaris, the Digital Mycology school coordinates the content and quality of this program. The academic director of each intake is named in the intake guide.
8.2Faculty
Taught by professionals who work in the field. The instructor for each intake is confirmed before the start.
Meet our faculty →Certificate
9.1Certificate awarded
Course Certificate
On completing the program and its project, Fungaris issues a Course Certificate. Fungaris certificates are the institute's own. Whether an employer, school or authority recognizes them depends on that organization and on local rules in each country.
9.2Issuing body / recognition
Issued by Fungaris (operated by Nexora Generation, S.L.) as a digital certificate. It is a Fungaris certificate of its own: it is not an official university degree and does not award ECTS credits.
About our certificates →Admission and enrollment
10.1Admission process (steps)
- Send your request through the form or write to admissions.
- Admissions reviews your profile and confirms the start date, the session schedule and the fee.
- You secure your place with full payment or a 40% reservation.
- You receive your campus access and welcome guide before the first session.
10.2Documents required
- A valid identity document.
- Contact and billing details (personal or company).
10.3Deadlines
Enrollment for the intake starting on January 11, 2027 is open until January 4, 2027, or until the group is full (maximum 20 students).
10.4Fee and payment options
Fee: $450
- Full payment before the start: $360 (20% reduction).
- 40% reservation ($180) and 3 monthly installments of $90.
10.5Grants, discounts and funding
Discounts: 10% for Fungaris alumni and 15% for groups of three or more people from the same organization. Discounts cannot be combined with each other or with the full-payment reduction.
Your employer can pay for the program and receive the invoice in the company name. Whether a public or employer training budget can cover the fee depends on your country, so check with them.
10.6Cancellation policy
The conditions for canceling, withdrawing or moving to a later intake are explained in our cancellation policy and in your enrollment confirmation. Nothing there limits your rights under the consumer law that applies to you.
Cancellation and refunds →Additional information
11.1Frequently asked questions
Do I need experience to study Digital Microscopy and Automated Spore Analysis?
Basic experience with a light microscope is recommended; a microscope camera is helpful but sample images are provided.
How is Digital Microscopy and Automated Spore Analysis taught?
Live online, in 6 modules with a working professional, a small group and a final project.
How am I assessed?
Progress is assessed through participation in live sessions, image analysis exercises in each module and a final project reviewed by the instructor.
What is the final project?
A calibrated, documented image set with semi-automated spore measurements or counts for a chosen group or trap sample.
What certificate do I get?
On completing the program and its project, Fungaris issues a Course Certificate. Fungaris certificates are the institute's own. Whether an employer, school or authority recognizes them depends on that organization and on local rules in each country.
What can I study after Digital Microscopy and Automated Spore Analysis?
The natural next step is Diploma in Fungal Bioinformatics.
11.2Alumni testimonials
We only publish verified testimonials from real students. This program does not have any published yet; they will appear here once its first intakes finish.
11.3Admissions contact
Write to info@fungaris.institute or use the contact form. Admissions answers in your language.
Keep branching.
Join the next intake.
Pay in full with a 20% reduction, or reserve your place with 40% and pay the rest in monthly installments. All prices are stated in US dollars (USD).