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Unraveling the complexity of the human breast | © EPFL – Patrik Aouad | The human breast epithelium comprises of an inner luminal and an outer myoepithelial, both embedded in a fibrous stroma. In order to study the cellular architecture in a 3D manner, breast tissue from healthy women who had undergone a reduction mammoplasty was immunostained for Cytokeratin-7 (Red) and Smooth Muscle Actin (Green) to distinguish the luminal and myoepithelial layers, respectively. Tissue was then subjected to 3D imaging after optical clarity, and reconstructed with Imaris Software.The grass is always greener in the next cell | © EPFL – Tamara Rossy and Alexandra Iouranova | Immunofluorescence staining of human bronchial epithelial cells grown at the air-liquid interface to mimic the conditions they encounter in the lungs. Upon differentiation, these cells grow cilia, which can be visualized using an anti-tubulin antibody (green), making them look like a field of grass. Actin and nuclei were counterstained (magenta and blue). We use this model to investigate different diseases, like ciliopathies and bacterial infections.The Bone Marrow: The RGB Mosaic | © EPFL – Ibrahim Bekri and Frédérica Schyrr | Mouse Bone Marrow composition quantified using an in-house developed ImageJ plugin. H&E stained bone marrow samples were scanned for further processing. The ImageJ plugin uses morphological operations as well as different thresholds to segment the image into different cell compartments of the bone marrow. The RGB mosaic was created using randomly generated RGB colors to represent each compartment of the bone marrow.Growing fat in 3D: Differentiating adipocytes on tissue engineered scaffolds | © EPFL – Daniel Naveed Tavakol | Tissue-engineered construct for culturing 3D adipocytes in vitro for regenerative medicine applications. Using mesenchymal stromal cells tagged with green fluorescent protein, we differentiated these immature cells into adipocytes, and stained their lipid droplets using LipidTox (magenta). These cells are attached to a scaffold (blue), which allows for the cells to stay adhered to the matrix during culture/imaging. This picture was taken on a Zeiss LSM 700 Microscope.Carnival of colours | © EPFL – Stefano Vianello | What happens when you put mouse embryonic stem cells in a drop of medium, and then leave them in the incubator? They self-organize! In few days the cells find each other, form a ball, break symmetry, and start elongating. By looking at the patterns generated we see that they mimic many steps of early mouse development without having to use real embryos! The collection you see here is stained for many different proteins. Can you guess which one marks the tail? Which ones are breaking symmetry?Convallaria…. or Lily of Valley | © EPFL – Thierry Laroche | Convallaria rhizome fine cuts stained with carmine-iodine green; Image acquisition with the DM5500B microscope in Fluorescence mode, in 3 channels (DAPI / GBP and RBP filters) with 20×075 HC PL APO CS lens and in Tille scan.Neuronal Net | © EPFL – Graham Knott | This is a scanning electron microscope (SEM) image of axons and dendrites crossing each other on the surface of a culture dish. This sample, supplied by the laboratory of Professor Hilal Lashuel, and prepared by the BioEM Facility was part of a project to understand how best to preserve and prepare cultured cells for imaging at high resolution with SEM. The field of view is 10 microns.Gigantic bacterial virus AR9 | © EPFL – Sergey Nazarov | Electron microscopy image of jumbo bacterial virus AR9 in vitreous ice at 80 000 magnification. Reconstructed Neuronal Connections | © EPFL – Anne Jorstad | 3D model showing axons in blue and dendrites in gray reconstructed from serial electron microscopy images taken from the cerebral cortex of the adult mouse. Contained in one axon are all the synaptic vesicles (yellow) and the endoplasmic reticulum (brown). This model was made as part of an analysis investigating the structure of different types of synaptic contacts.Rainbow Urchin | © EPFL – Romain Guiet | The day after plating,HELA cells were fixed and stained for F-actin using Phalloidin. A Z-stack was acquired on an Zeiss LSM710 confocal microscope (Voxel size 28x28x130nm) using a 63x oil objective (NA 1.4) and deconvolved using the Huygens software(CMLE, SNR 10, Quality threshold. 0.1). To obtain the submitted image a color-coded projection was applied using the Lookup Table Physics.What Makes Our (Mini)Brains Human? | © EPFL – Christopher Playfoot | Cerebral organoids or mini brains provide a window into the processes governing early human brain development. By both understanding and perturbing these processes, we aim to unravel what makes our brains human. Shown here is the internal, self-organised structure of an immature human cerebral organoid, derived from human embryonic stem cells. Rosettes of neural progenitor SOX2 positive radial glia (red) are interspersed with TUJ1 positive newborn neurons (green). Nuclei are marked in blue.T cell decorated with polymer nanoparticles | © EPFL – Tanja Thomsen | Confocal fluorescent microscopy was used to show a T cell which surface is decorated with 200 nm sized biodegradable fluorescent polymer nanoparticles. The cell cytosol is stained with CellTrace Violet and the membrane with WGA Texas Red. In cell mediated drug delivery the modification of cell surfaces with drug-loaded polymer nanocarriers via different covalent and non-covalent methods presents a potential strategy to enhance drug targeting by taking advantage of intrinsic cellular properties.Top view of human centriole | © EPFL – Skvortsova Mariya Yuryevna | Super-resolution STED z-stack of delta and acetylated tubulin of RPE-1 cells after expansion microscopyCeci n’est pas une grille. | EPFL © Nicolas Chiaruttini | A vertical grid is placed on a microscope and illuminated by a white light source. This image, taken with a color camera, is the diffraction pattern observed on the rear focal plane of the objective. The EPFL’s BIOP core facility has a simple and “open” educational microscope. Optical paths can be modified and imaged in various ways, in order to facilitate the teaching of the underlying principles of optical microscopy.Am I a brain? | © EPFL – Jessica Dessimoz | Tissue paraffin section stained with Picrosirius Red under transmitted and polarized light. To find out if the image represents a brain or not please see Jessica right next to the exposition.Brain Onion | © EPFL – Michael Kintscher | Shown is a fluorescence image of retrogradely labeled neurons in the nucleus of the lateral olfactory tract (LOT). The injection was done on the contralateral hemisphere in the basolateral amygdala (BLA) using a mix of an AAVretro expressing GFP (red) and a Cholera Toxin Subunit B/Alexa 647 Conjugate (green). The experiment was done in order to label brain regions that provide input to the BLA, but also to compare the uptake properties/tropism of the two retrograde labeling techniques.EnLighting memories | © EPFL – Lucie Dixsaut | We aim at understanding the neuronal circuits involved in longterm memory storage. I injected two fluorescent retrograde tracers in the prelimbic cortex, one in each hemisphere of the brain, in order to visualize all the regions that send projections to this area, known to be implicated in the storage of old memories. In this 20 μm thick brain slice, all cell nuclei in blue (post-slicing Hoechst staining) and the two fluorescent tracers in pink and yellow are visible.Image showing lung surfactant captured with a transmission electron microscope | © EPFL – Stéphanie Clerc-Rosset | Lamellar bodies (dark blobs) give rise to the square lattice network that characterises tubular myelin in the extracellular space of lung tissues. These are components of surfactant secreted by type-II pneumocytes into the alveoli. In this specific case, lamellar bodies are produced and their content secreted from lung tumour cells. Width of image is 3 microns. Image taken by BioEM Facility for the research project of Caroline Contat in the laboratory of Professor Etienne Meylan.When cGAS binds to nuclear DNA | © EPFL – Baptiste Guey | cGAS is a DNA sensor which is able to detect cytosolic DNA particles. Thus, during viral infection, cGAS binds viral DNA and activates an inflammatory response to fight the infection. However, it turns out that cGAS is not only able to detect exogenous DNA but also endogenous DNA. This immuno-staining shows cGAS protein (green) that penetrates and binds DNA (red) after nuclear envelope rupture. Our research goal is to determine whether cGAS elicits inflammation after such events.Glutamate in the Cerebral Cortex | © EPFL – Jérôme Blanc | A reconstruction of all the 30,441 vesicles (yellow) and astrocytic elements (blue) in a cube of tissue from the cerebral cortex of an adult mouse (total volume 91 cubic microns). The model was made as part of an analysis to understand the distribution of synaptic vesicles in different types of neurons, and brain regions. 
Unraveling the complexity of the human breast | © EPFL – Patrik Aouad | The human breast epithelium comprises of an inner luminal and an outer myoepithelial, both embedded in a fibrous stroma. In order to study the cellular architecture in a 3D manner, breast tissue from healthy women who had undergone a reduction mammoplasty was immunostained for Cytokeratin-7 (Red) and Smooth Muscle Actin (Green) to distinguish the luminal and myoepithelial layers, respectively. Tissue was then subjected to 3D imaging after optical clarity, and reconstructed with Imaris Software.
The grass is always greener in the next cell | © EPFL – Tamara Rossy and Alexandra Iouranova | Immunofluorescence staining of human bronchial epithelial cells grown at the air-liquid interface to mimic the conditions they encounter in the lungs. Upon differentiation, these cells grow cilia, which can be visualized using an anti-tubulin antibody (green), making them look like a field of grass. Actin and nuclei were counterstained (magenta and blue). We use this model to investigate different diseases, like ciliopathies and bacterial infections.
The Bone Marrow: The RGB Mosaic | © EPFL – Ibrahim Bekri and Frédérica Schyrr | Mouse Bone Marrow composition quantified using an in-house developed ImageJ plugin. H&E stained bone marrow samples were scanned for further processing. The ImageJ plugin uses morphological operations as well as different thresholds to segment the image into different cell compartments of the bone marrow. The RGB mosaic was created using randomly generated RGB colors to represent each compartment of the bone marrow.
Growing fat in 3D: Differentiating adipocytes on tissue engineered scaffolds | © EPFL – Daniel Naveed Tavakol | Tissue-engineered construct for culturing 3D adipocytes in vitro for regenerative medicine applications. Using mesenchymal stromal cells tagged with green fluorescent protein, we differentiated these immature cells into adipocytes, and stained their lipid droplets using LipidTox (magenta). These cells are attached to a scaffold (blue), which allows for the cells to stay adhered to the matrix during culture/imaging. This picture was taken on a Zeiss LSM 700 Microscope.
Carnival of colours | © EPFL – Stefano Vianello | What happens when you put mouse embryonic stem cells in a drop of medium, and then leave them in the incubator? They self-organize! In few days the cells find each other, form a ball, break symmetry, and start elongating. By looking at the patterns generated we see that they mimic many steps of early mouse development without having to use real embryos! The collection you see here is stained for many different proteins. Can you guess which one marks the tail? Which ones are breaking symmetry?
Convallaria…. or Lily of Valley | © EPFL – Thierry Laroche | Convallaria rhizome fine cuts stained with carmine-iodine green; Image acquisition with the DM5500B microscope in Fluorescence mode, in 3 channels (DAPI / GBP and RBP filters) with 20×075 HC PL APO CS lens and in Tille scan.
Neuronal Net | © EPFL – Graham Knott | This is a scanning electron microscope (SEM) image of axons and dendrites crossing each other on the surface of a culture dish. This sample, supplied by the laboratory of Professor Hilal Lashuel, and prepared by the BioEM Facility was part of a project to understand how best to preserve and prepare cultured cells for imaging at high resolution with SEM. The field of view is 10 microns.
Gigantic bacterial virus AR9 | © EPFL – Sergey Nazarov | Electron microscopy image of jumbo bacterial virus AR9 in vitreous ice at 80 000 magnification. 
Reconstructed Neuronal Connections | © EPFL – Anne Jorstad | 3D model showing axons in blue and dendrites in gray reconstructed from serial electron microscopy images taken from the cerebral cortex of the adult mouse. Contained in one axon are all the synaptic vesicles (yellow) and the endoplasmic reticulum (brown). This model was made as part of an analysis investigating the structure of different types of synaptic contacts.
Rainbow Urchin | © EPFL – Romain Guiet | The day after plating,HELA cells were fixed and stained for F-actin using Phalloidin. A Z-stack was acquired on an Zeiss LSM710 confocal microscope (Voxel size 28x28x130nm) using a 63x oil objective (NA 1.4) and deconvolved using the Huygens software(CMLE, SNR 10, Quality threshold. 0.1). To obtain the submitted image a color-coded projection was applied using the Lookup Table Physics.
What Makes Our (Mini)Brains Human? | © EPFL – Christopher Playfoot | Cerebral organoids or mini brains provide a window into the processes governing early human brain development. By both understanding and perturbing these processes, we aim to unravel what makes our brains human. Shown here is the internal, self-organised structure of an immature human cerebral organoid, derived from human embryonic stem cells. Rosettes of neural progenitor SOX2 positive radial glia (red) are interspersed with TUJ1 positive newborn neurons (green). Nuclei are marked in blue.
T cell decorated with polymer nanoparticles | © EPFL – Tanja Thomsen | Confocal fluorescent microscopy was used to show a T cell which surface is decorated with 200 nm sized biodegradable fluorescent polymer nanoparticles. The cell cytosol is stained with CellTrace Violet and the membrane with WGA Texas Red. In cell mediated drug delivery the modification of cell surfaces with drug-loaded polymer nanocarriers via different covalent and non-covalent methods presents a potential strategy to enhance drug targeting by taking advantage of intrinsic cellular properties.
Top view of human centriole | © EPFL – Skvortsova Mariya Yuryevna | Super-resolution STED z-stack of delta and acetylated tubulin of RPE-1 cells after expansion microscopy
Ceci n’est pas une grille. | EPFL © Nicolas Chiaruttini | A vertical grid is placed on a microscope and illuminated by a white light source. This image, taken with a color camera, is the diffraction pattern observed on the rear focal plane of the objective. The EPFL’s BIOP core facility has a simple and “open” educational microscope. Optical paths can be modified and imaged in various ways, in order to facilitate the teaching of the underlying principles of optical microscopy.
Am I a brain? | © EPFL – Jessica Dessimoz | Tissue paraffin section stained with Picrosirius Red under transmitted and polarized light. To find out if the image represents a brain or not please see Jessica right next to the exposition.
Brain Onion | © EPFL – Michael Kintscher | Shown is a fluorescence image of retrogradely labeled neurons in the nucleus of the lateral olfactory tract (LOT). The injection was done on the contralateral hemisphere in the basolateral amygdala (BLA) using a mix of an AAVretro expressing GFP (red) and a Cholera Toxin Subunit B/Alexa 647 Conjugate (green). The experiment was done in order to label brain regions that provide input to the BLA, but also to compare the uptake properties/tropism of the two retrograde labeling techniques.
EnLighting memories | © EPFL – Lucie Dixsaut | We aim at understanding the neuronal circuits involved in longterm memory storage. I injected two fluorescent retrograde tracers in the prelimbic cortex, one in each hemisphere of the brain, in order to visualize all the regions that send projections to this area, known to be implicated in the storage of old memories. In this 20 μm thick brain slice, all cell nuclei in blue (post-slicing Hoechst staining) and the two fluorescent tracers in pink and yellow are visible.
Image showing lung surfactant captured with a transmission electron microscope | © EPFL – Stéphanie Clerc-Rosset | Lamellar bodies (dark blobs) give rise to the square lattice network that characterises tubular myelin in the extracellular space of lung tissues. These are components of surfactant secreted by type-II pneumocytes into the alveoli. In this specific case, lamellar bodies are produced and their content secreted from lung tumour cells. Width of image is 3 microns. Image taken by BioEM Facility for the research project of Caroline Contat in the laboratory of Professor Etienne Meylan.
When cGAS binds to nuclear DNA | © EPFL – Baptiste Guey | cGAS is a DNA sensor which is able to detect cytosolic DNA particles. Thus, during viral infection, cGAS binds viral DNA and activates an inflammatory response to fight the infection. However, it turns out that cGAS is not only able to detect exogenous DNA but also endogenous DNA. This immuno-staining shows cGAS protein (green) that penetrates and binds DNA (red) after nuclear envelope rupture. Our research goal is to determine whether cGAS elicits inflammation after such events.
Glutamate in the Cerebral Cortex | © EPFL – Jérôme Blanc | A reconstruction of all the 30,441 vesicles (yellow) and astrocytic elements (blue) in a cube of tissue from the cerebral cortex of an adult mouse (total volume 91 cubic microns). The model was made as part of an analysis to understand the distribution of synaptic vesicles in different types of neurons, and brain regions.
