Image J/ Fiji

* How to re-align 3 or 4 fluorescence channels? (Source: G. Landini, University of Birmingham, UK)

Align 4 plugin

Align RGB

Plugins to download HERE

* Manuel d'analyse d'images avec le logiciel ImageJ (French) (source: Sophie Allart and Astrid Canivet, Inserm, TRI-Genotoul imagerie, France)
Manuel ImageJ
 * Analyzing Fluorescence microscopy images with ImageJ (source: Peter Bankhead, Queen's Univ. Belfast) Analyzing Fluo
* Scientific Image Analysis: the world Image J (French)
(source: Daniel Sage, EPFL-STI, BIG, Lausanne, Switzerland)
* How to calibrate the pixel size in microns and how to add a scale bar to my image? Calibration & Scale Bar
* How to determine the intensity profil of three different channels? Intensity Profil
* How to count cell nuclei on a confocal image? Nuclei Counting
* Image processing and analysis: introduction (source: Montpellier RIO imaging, France) Basics.pdf
* Opening multi-format files with the LOCI Bio-Format plugin (source: Chicago Univ., USA) LOCI.pdf
* Merging colors beyond RGB (source: Chicago Univ., USA) Merge.pdf
* Making montages (source: Chicago Univ., USA) Montage.pdf
* Basic cell counting (source: Chicago Univ., USA) CellCounting.pdf
* Counting objects by template matching (source: Chicago Univ., USA) ObjectCounting.pdf
* Basic image quantification from images (source: Chicago Univ., USA) Quantification.pdf
* Manual tracking (source: Curie Institute, Paris, France) Tracking.pdf
* Quantification of gel images GelAnalysis.pdf
* Colour analysis tools (Auckland univ., New Zealand) ColourAnalysis.pdf


* How to use the trainable Weka Segmentation plugin of Fiji to segment color images into three different types of regions (machine learning)?



* How to work with a large image acquired with the VS120 Olympus?

(source: O.Burri,R. Guiet, BIOP, EPFL, Lausanne, Switzerland)

VSI Reader Actionbar


* How to analyze a colocalization?

(source: F. Cordelières, S. Bolte, Paris, France)


Wiki doc

* How to track microscopes' performances ?

(source: F. Cordelières/ Paris C. Matthews/ Marseille, France)




* How to detect filopodia ? (source: Guillaume Jacquemet and Alexandre Carisey)