Table 2. Examples of open-source toolboxes, components and workflows used during NEUBIAS TSs.
These, and many others, are catalogued in Biii.eu with links to access the training materials from public repositories such as Zenodo and Github.
| Toolboxes/languages | Used for training | Level(s) | NEUBIAS TSs |
|---|---|---|---|
| CellProfiler & Analyst | IA intro & workflows | basic, advanced | TS2,4,6,8,10,12,14 |
| Drishti | 3D visualization | basic | TS6 |
| Icy | IA intro & workflows | basic, advanced, scripting | TS2,3,6 |
| Ilastik | Workflows | basic, advanced | TS7,9,14 |
| ImageJ/FIJI | IA intro, workflows & scripting | basic, advanced, scripting | all |
| KNIME | IA intro & workflows | basic | TS3,5 |
| MatLab | IA intro, workflows & scripting | basic, advanced, scripting | TS1,3,5,6,9 |
| OMERO | Workflows | basic | TS9 |
| Python/scikit-image | Workflows & scripting | basic, scripting | TS5,13,15 |
| QuPath | Workflows | basic | TS8,9 |
| R | Workflows & analysis | basic | TS10,12 |
| Components | |||
| BigDataViewer | BIA of large datasets | basic | TS6,7,9,10,13 |
| BigStitcher | IP of large datasets | advanced | TS9,10,12,14 |
| ClIJ | IP workflows | basic, advanced | TS13,14 |
| DeconvolutionLab | IP | basic | TS2 |
| FigureJ | Figures for publication | basic | TS2,4,8,14 |
| Filters & morpho. operators | IP techniques | basic, advanced, scripting | TS1,2,3,4,6,10,12,14 |
| Imglib2/API | Development | advanced | TS11,13 |
| SR-Tesseler | Analysis workflows | advanced | TS3 |
| TrackMate/Mastodon | Tracking workflows | basic, advanced | TS5,6,7,8,10,13,14 |
| Workflows | |||
| 3D Tubular Networks | Analysis workflows | advanced, scripting | TS1 |
| Colocalization and clustering | Analysis workflows | basic, advanced | TS1,3,7,11,12,14 |
| Machine Learning | IP workflows | basic, advanced, scripting | TS4,6,10,11,12,13,14,15 |
| Particle analysis | Segmentation & analysis | basic, advanced | all |
| Segmentation | Analysis workflows | basic, advanced, scripting | TS1,2,4,5,6,79,10,12,13 |
| SurfCut | IP workflows | advanced | TS15 |
| Tracking | Analysis workflows | basic, advanced | TS1,3,5,6,7,8,9,10,12,13,14 |
| Other topics | |||
| Intro to bioimages | Data quality | all | TS2,12 |
| Natural History of Fake Data | Ethics in BIA | all | TS2,4,6,7,10,12,14 |
| P-value hacking | Ethics in BIA | all | TS15 |
| Resources for Analysis | Review of tools | advanced | TS3,11,14 |
| The Software Jungle | Review of tools | basic | TS14 |