Gilles Carpentier Research Web Site: Computer Image Analysis
Image analysis tools in biology and biochemistry using ImageJ

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Wednesday 21 October 2015, by Gilles Carpentier

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- LFM-init-rec: Lensfree raw acquisition of human umbilical vein endothelial cells cultured on Matrigel. The field of view is 29.4 mm2

- LFM-treated-rec: Holographic reconstruction of the recorded image shown in (a). The results is a modulus image which depicts the cells in dark gray over a light grey background.

The holographic reconstruction consists first in back-propagating the light intensity recorded by the sensor through the Fresnel function. The recovered complex image is however strongly affected by the so-called ‘twin image’, an artefact that results from a lack of phase information in the acquisition process. To retrieve the phase in the sensor plane and consequently diminish the ‘twin-image’ artefact in the reconstructed images, we used a phase-retrieval algorithm. The purpose of such an algorithm is to recover the complex image of the sample from the phase-less recorded holographic image. It allows to refine the estimate of the complex image in the sensor plane by iteratively applying update rules in a gradient descent scheme.

Credits : Cell culture: F.Navarro (ab), M. Menneteau (ab), Holographic reconstruction: L. Hervé (ab), C. Allier (ab), a Univ. Grenoble Alpes, F‐38000 Grenoble, France. b CEA LETI MlNATEC Campus, F-38054 Grenoble, France.

- LFM-analyzed-rec: Image " LFM-treated-rec" analyzed by a customized version of the Angiogenesis Analyzer.

- microcosme2: Fluorescent algae and other microorganisms. Olympus IX80 microscope coupled to an ORCA R2 Hamamatsu CCD camera. Sample source; Iglika Christova, image acquisition and processing, Gilles Carpentier.

- lens-free-init2 (HUVEC Lensfree Microscopy), and lens-free-obj2 (HUVEC Lensfree Microscopy + Analysis). HUVEC network acquired by lens free microscopy and analyzed by a cutomized version of the Angiogenesis Analyzer. Details and timelapse here.

- NiceCells2 (Fluorescent Cell - Tubulin labeling (green)) Image source : slide through the courtesy of Angelica Keller, image acquisition from the author. BH2 Olympus microscope and Scion CCD CFW-1310M Camera. Project link.

- Huvec Phase Contrast, Huvec Phase Contrast + Analysis, Huvec Fluo, Huvec Fluo + Analysis, are huvec networks analyzed with the Angiogenesis Analyzer.

- HistoMuscle-4Channels and HistoMuscle-3Channels : Muscle slice; immunolabeling from Elisa Negroni, image acquisition from Emilie Henault. IX81 inverted Olympus microscope and Orca Hamamatsu R2 CCD camera. Project link.

- Myoblast-init-2, Myoblast-init-Deblured-2, Myoblast-init-Deblured-fft-fft-2 : Different improvements of a laser scanning transmission image. Image from the author. Project link.

- Nerve image from the courtesy of Dr  Brigitte Blondet. Device for the image acquisition: monochrome CMOS Sound Vision camera mounted onto an Olympus BH-2 microscope. Project link

- Rat myotube culture immunostaining. The example contains a triple labeling of a differentiated mouse myogenic cell line. Cell culture and immunochemistry; Juliette Peltzer, images from the courtesy of Dr Angelica Keller. Project links, here and here.

- « Array » and « Analyzed Array » are protein arrays analyzed by the Protein Array Analyzer, ImageJ conference.

logoij ImageJ ( is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. The author, Wayne Rasband (, is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.
Gilles Carpentier, Faculte des Sciences et Technologie,
Universite Paris Est Creteil Val-de-Marne, France.

Special thanks to Alessandra Albano for the English correction of these sites.
Computer Data Acquisition
for Biochemistry Practice Works
Image analysis tools in biology
and biochemistry using ImageJ
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