France BioImaging training initiative

Explore, reuse and build bioimaging training resources

FBI-Training connects structured knowledge, reusable training sheets and community-built courses in one shared training environment.

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Knowledge Books

Explore bioimaging knowledge through structured expert ontologies and their relationships.

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Training sheets

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FBI-Training

Why this portal?

FBI-Training connects ontology concepts, reusable FAIR training sheets and structured community courses while preserving versions, credits and provenance.

Inside the Knowledge Books

FAQ

How do Knowledge Books, training sheets and courses fit together?

Knowledge Books organise bioimaging concepts. Training sheets are reusable learning resources attached to those concepts. Community courses assemble selected published sheet revisions into structured learning paths while preserving their credits and provenance.

Published training sheet

Introduction and working space

EM-001-005-0001-C · v01.01

Learning aim

We will give you details of all the different steps of ultramicrotomy:

Abstract

France BioImaging Training - MOOC Series - ULTRAMICROTOMY AT ROOM TEMPERATURE - TEXTE TEASER L’ultramicrotomie est une étape essentielle pour tout microscopiste électronique ! En effet, la plupart des échantillons biologiques sont bien trop épais pour être observés tels quels au microscope électronique en transmission. Il est donc indispensable de réaliser des coupes de ces échantillons…

Content preview

France BioImaging Training - MOOC Series - ULTRAMICROTOMY AT ROOM TEMPERATURE - TEXTE TEASER L’ultramicrotomie est une étape essentielle pour tout microscopiste électronique ! En effet, la plupart des échantillons biologiques sont bien trop épais pour être observés tels quels au microscope électronique en transmission. Il est donc indispensable de réaliser des coupes de ces échantillons pour pouvoir les observer au MET. La formation à l’ultramicrotomie nécessite beaucoup de pratique, ce MOOC vous donnera les bases théoriques pour aborder cette technique et sera un précieux support lors de la mise en pratique sur l’ultramicrotome. Nous allons donc vous présenter dans ce MOOC toutes les étapes nécessaires à la réalisation de coupes. Nous allons parler des coupes d’échantillons une fois qu’ils…

Ontology context

Introduction and working space

Keywords

electron microscopyintroductionroom temperatureultramicrotomy

Published training sheet

Raw trimming

EM-001-005-0002-C · v01.01

Learning aim

The sample block must be prepared in a way that the area of interest is on the surface of the block in a small area of about 1 X 1 mm or even smaller.…

Abstract

3 RAW Trimming The sample block must be prepared in a way that the area of interest is on the surface of the block in a small area of about 1 X 1 mm or even smaller. The block containing the sample will be ready to be finely trimmed and polished for ultra-thin sectioning.

Content preview

RAW Trimming Objective The sample block must be prepared in a way that the area of interest is on the surface of the block in a small area of about 1 X 1 mm or even smaller. The block containing the sample will be ready to be finely trimmed and polished for ultra-thin sectioning. General notions Samples for ultramicrotomy are generally included in the Epon resin which cures the sample and sample block. A saw (cf. Figure 3.2.1) can be used in order to separate the sample block in different parts, to remove big portions of empty resin or to reach the core part of a tissue of interest. Sample block can be sawn with a jewelers saw Afterwards the…

Ontology context

Raw trimming

Keywords

electron microscopyraw trimmingroom temperatureultramicrotomy

Published training sheet

Fine trimming

EM-001-005-0003-C · v01.01

Learning aim

The goal of fine trimming is to polish the sample surface and to trim the four sides of the pyramid to obtain a very small cutting area that allows the cutting of ultrathin sections.

Abstract

4 Fine trimming The goal of fine trimming is to polish the sample surface and to trim the four sides of the pyramid to obtain a very small cutting area that allows the cutting of ultrathin sections. In the first step of fine trimming, the sample surface should be polished and reflect light like a mirror.…

Content preview

Fine trimming Objective The goal of fine trimming is to polish the sample surface and to trim the four sides of the pyramid to obtain a very small cutting area that allows the cutting of ultrathin sections. General notions In the first step of fine trimming, the sample surface should be polished and reflect light like a mirror. This will help later with alignment of the blockface to the knife edge. In the second step of fine trimming, the four sides are shaped to form a pyramid with slopes of 45° to 60°. Top and bottom edges of the sample surface must be parallel. The top of the pyramid (or the blockface) has the shape of a trapezoid, a rectangle…

Ontology context

Fine trimming

Keywords

electron microscopyfine trimmingroom temperatureultramicrotomy

Published Community course

Room-temperature ultramicrotomy

COURSE-DEMO-005 · version 1

Course summary

A complete room-temperature ultramicrotomy pathway from workspace preparation and trimming to section recovery and knife cleaning.

Course outline

  1. § Room-temperature ultramicrotomy workflow
  2. S Introduction and working spaceEM-001-005-0001-C · v01.01 · EN
  3. S Raw trimmingEM-001-005-0002-C · v01.01 · EN
  4. S Fine trimmingEM-001-005-0003-C · v01.01 · EN
  5. S Fine approach and alignmentEM-001-005-0004-C · v01.01 · EN
  6. S Preparation of the knifeEM-001-005-0005-C · v01.01 · EN
  7. S SectioningEM-001-005-0006-C · v01.01 · EN
  8. S Picking up sectionsEM-001-005-0007-C · v01.01 · EN
  9. S Cleaning of knife and working stationEM-001-005-0008-C · v01.01 · EN

Keywords

electron microscopyultramicrotomyroom temperaturetrimmingsectioning

Published Community course

Foundations of bioimage analysis

COURSE-DEMO-001 · version 1

Course summary

A beginner-friendly route from microscopy quality control to the first segmentation concepts.

Course outline

  1. § From image quality to analysis
  2. S Identify chromatic aberrations in fluorescence microscopyLM-001-001-0001-C · v01.01 · EN
  3. S Thresholding: separating objects from backgroundIP-001-001-0001-C · v01.01 · EN

Keywords

bioimage analysismicroscopysegmentationfundamentals

Published Community course

Practical thresholding workshop

COURSE-DEMO-002 · version 1

Course summary

A short practical course focused on threshold-based segmentation, limits and interpretation.

Course outline

  1. § Hands-on segmentation
  2. S Thresholding: separating objects from backgroundIP-001-001-0001-C · v01.01 · EN

Keywords

thresholdingsegmentationpracticalImageJ