Author Archives: Marco Barnig

Télémanipulateur chirurgical da Vinci

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Last update : 7 mars 2017

Le télémanipulateur chirurgical da Vinci est une plate-forme chirurgicale de pointe, équipée d’une vision 3D haute définition et de micro-instruments chirurgicaux articulés, conçue pour aider les chirurgiens à dépasser les limites de la chirurgie laparoscopique (invasion moyennant des petites incisions) et effractive conventionnelle. Le système est fabriqué par la société américaine Intituitive Surgical.

Télémanipulateur chirurgical da Vinci

Télémanipulateur chirurgical da Vinci

Bien que souvent appelé robot, le système da Vinci ne peut pas agir tout seul ; l’intervention est entièrement effectuée par un chirurgien, du début à la fin. Le système se compose de deux consoles : un pupitre de commande (joystick), avec vision en 3D haute définition, et un manipulateur avec quatre bras.

Plus que 2.000 systèmes ont été vendus jusqu’à présent, dont la majorité aux Etats-Unis. Le prix de vente d’un système avoisine 2 millions de dollars.

Parmi les avantages du système on rapporte que les opérations sont moins invasives pour le patient, que le chirurgien se fatigue moins (le système évite des tendinites au chirurgien) et que les tremblements de la main n’ont pas d’effet sur l’opération. Les inconvénients sont les frais élevés, l’apprentissage difficile de la manipulation du système et l’absence de la sensation tactile au chirurgien lorsque les pinces touchent un organe. Sur les forums médicaux sur le web, des médecins et infirmiers qui travaillent à proximité d’un robot da Vinci témoignent que la durée d’une opération est deux à trois fois plus longue qu’une intervention chirurgicale laparoscopique classique.

Le Centre Hospitalier du Kirchberg est le premier établissement de santé Luxembourgeois à acquérir un télémanipulateur chirurgical da Vinci.

Des informations supplémentaires sont disponibles sur les sites web suivants :

ISO image

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Free ISO image Burner

Free ISO image Burner

An ISO image is an archive file of an optical disc, a type of disk image composed of the data contents of every written sector of an optical disc, including the optical disc file system. The name ISO is taken from the ISO 9660 file system used with CD-ROM media. ISO image files usually have a file extension of .iso. ISO images are uncompressed and do not use a particular container format; they are a sector-by-sector copy of the data on an optical disc, stored inside a binary file.

ISO images can be created from optical discs by disk imaging software, from a collection of files by optical disc authoring software, or from a different disk image file by means of conversion. Software distributed on bootable discs (fox exampe Linux Debian) is often available for download in ISO image format.

ISO burner

To burn an ISO image to a CD or DVD, you need a disc image burner software. There are several such tools available. I use Free ISO Burner from SoftSea. This program is very simple and easy to use and hide all complex settings. The current version is 1.2, released on January 10, 2011.

HDR : high-dynamic-range imaging

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Last update : December 25, 2021

HDR (High-dynamic-range imaging) is a set of methods used in imaging and photography to capture a greater dynamic range between the lightest and darkest areas of an image than current standard digital imaging methods or photographic methods. The two main sources of high-dynamic-range images are computer renderings and merging of multiple standard-dynamic-range (SDR) photographs created with exposure bracketing.

As the popularity of the HDR imaging method increased in the last years, several camera manufactures are now offering built-in high-dynamic-range features. HDR is also integrated in new smartphones. Since iOS4.1, Apple iPhones have a built-in HDR functionality. Android launched HDR mode for the camera app in version 4.2 (Jelly Bean); Blackberry introduced HDR in the Z10 with OS update 10.1.

hdr

HDR Photo by Jon Rutlen on Flickr

A very detailed contribution about concepts, standards and related aspects of HDR has been published by Digiarty Software Inc. The following links provide some ancient information about HDR :

Subtitles in mp4 video files

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Last update : September 22, 2013

Subtitles

Subtitles are textual versions of the dialog in films and television programs, usually displayed at the bottom of the screen. They can either be a form of written translation of a dialog in a foreign language, or a written rendering of the dialog in the same language, with or without added information to help viewers to follow the dialog.

Closed Captioning

Another process of displaying text on a visual display to provide additional or interpretive information is called closed captioning (CC). Most people don’t distinguish captions from subtitles. In the United States and Canada (ATSC), these terms do have different meanings. Closed captions were created for the deaf community or hard of hearing individuals to assist in comprehension. Everything you purchase from Apple’s iTunes Store have CC subtitles, if at all. CC subtitles can be extracted with CCextractor (version 0.66 released on July 1, 2013), a free GPL licensed closed caption tool for Windows.

Read The Closed Captioning Bible by Werner Ruotsalainen about this topic.

SubRip

The most basic of all subtitle formats is SubRip, named with the extension .srt, which contains formatted plain text.

SRT consists of four parts :

  • A number indicating which subtitle it is in the sequence
  • The time that the subtitle should appear on the screen, and then disappear
  • The subtitle itself
  • A blank line indicating the start of a new subtitle

Here is an example :

1
00:00:20,000 --> 00:00:24,400
Altocumulus clouds occur between six thousand

2
00:00:24,600 --> 00:00:27,800
and twenty thousand feet above ground level.

Subtitle editor

Subtitle Workshop

Subtitle Workshop

There exist a great number of subtitle formats and programs to create subtitles. An efficient and convenient subtitle editing tool that supports all the subtitle formats you need and has all the features you would want from such a tool is Subtitle Workshop (version 6.0a released on August 26, 2013) from URUWorks. It even includes spell check function and an advanced video preview feature, but it doesn’t embed the subtitles in a video file.

Another performant tool is Subtitle Edit (version 3.3.8 released on September 1, 2013; Wikipedia) created by Nikolaj Lynge Olsson from Denmark.

Subtitle embedder

There exist two methods to embed subtitles in video files : soft embedding and hard burning. The following tools allow the embedding of SRT subtitles :

SRT subtitles are embedded with Timed Text as the Stream Text type, CC subtitles are labeled as EIA-608.

Subtitle player

The following players and servers support delivering of integrated subtitles :

Links

The following links provide additional informations about soft subtitles in videos :

File date before 1980

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Last update : September 16, 2013

If files have a date before 1980, Windows Explorer shows a blank in the date column. This is the case for the created, modified or picture taken date. Sorting files or pictures by their real date taken is impossible. The correct date is however displayed in the properties box.

I you have a photo or video collection, the fact that files with a date before 1980 are not sorted as expected is an awesome problem which has not yet been solved in Windows 8. Since Windows itself did not exist before 1980, there seems to be a problem with creation or last modified date and time for a file stamped before that time.

Date created gives us the information about when the file was moved to a specific location. Date modified is about the date when the file was last modifie. The modified date can be prior to the creation date of a file.

The picture taken date is saved in the Exif metadata of a picture file. For videos, there exist no similar standardized property. Videos encoded with Apple Quicktime are stamped with proprietary metadata com.apple.quicktime.creationdate. The file creation or modification dates are used as timestamp for avi, mp4 and MOV video files.

Most photo or video tools however manage files with a date before 1980 as expected. I tested the following applications :

  • Synology PhotoStation
  • Synology VideoStation

 

Anamorphic video

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The term anamorphic refers to a distorted image that appears normal when viewed with an appropriate lens. When shooting film or video, an anamorphic lens can be used to squeeze a wide image onto a standard 4:3 aspect ratio frame. During projection or playback, the image must be unsqueezed, stretching the image back to its original aspect ratio.

By default, 16:9 anamorphic video displayed on an standard monitor appears horizontally squeezed, meaning images look tall and thin. The advantage of this was in the past that producers could shoot wide-screen material using inexpensive equipment. Rescaling anamorphic video in order to see the entire wide screen frame on a standard definition 4:3 monitor is called letterboxing, and results in the loss of the maximum resolution available in the source footage. A wide screen (16:9) allows video-makers more room for creativity in their shot composition.

To check the support of anamorphic videos by different players, I created three mp4 videos from scratch, based on squeezed test pictures :

testbild_anamorphic

Source pictures  640×480, 854×480 and 1.280×480 squeezed to 640×480 pictures

The following ffmpeg script creates a video from a squeezed source image towards a stretched widescreen video with a ratio 2.35:1.

ffmpeg ^
-loop 1 ^
-f image2 ^
-i testbild_2_35_1_squeezed.jpg ^
-r pal ^
-vcodec libx264 ^
-aspect 235:100 ^
-crf 23 ^
-preset medium ^
-profile:v baseline ^
-level 3.1 ^
-refs 1 ^
-t 30 ^
testbild_anamorphic_2_35_1.mp4
pause

The -aspect parameter handles the correct display aspect ratio (DAR). The MediaInfo tool shows that the video has 640×480 pixels, but an DAR of 2.35:1.

MediaInfo

MediaInfo

The VLC video player stretches the video based on the DAR. Videos with a wrong DAR in the metadata can be resized manually by changing the aspect ratio in the corresponding video menu.

anamorphic video

VLC media player

More informations about anamorphic videos are available at the following links :

Human Brain Parts and Regions

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Last update : October 11, 2014

human brain regions

brain regions

The brain is the center of the nervous system in all vertebrate and most invertebrate animals. From a philosophical point of view, what makes the brain special in comparison to other organs is that it forms the physical structure that generates the mind. Through much of history, the mind was thought to be separate from the brain. Even for present-day neuroscience, the mechanisms by which human brain activity gives rise to consciousness and thought remain very challenging to understand: despite rapid scientific progress, much about how the human brain works remains a mystery. The operations of individual brain cells are now understood in considerable detail, but the way they cooperate in ensembles of millions has been very difficult to decipher.

The human brain has three main parts :

  1. The cerebrum, or telencephalon (Grosshirn, cerveau), that fills up most of the skull, is involved in cognition and also controls movement.
  2. The cerebellum, or little brain (Kleinhirn, cervelet), that sits at the back of the head, under the cerebrum, controls coordination and balance.
  3. The brainstem (Hirnstamm, tronc cérébral), that sits beneath the cerebrum in front of the cerebellum, connects the brain to the spinal cord and controls automatic functions such as breathing, digestion, heart rate and blood pressure.

The human brain is divided into right and left halves (hemispheres). The left half controls movement on the body’s right side. The right half controls the body’s left side. In most people, the language area is mainly on the left. Preserved brains have a grey color, hence the name grey matter.

The brain’s wrinkled surface is a specialized outer layer of the cerebrum, called the cerebral cortex (what we see when we look at the brain). Each bump on the surface of the human brain is known as a gyrus, while each groove is known as a sulcus.

In a typical human the cerebral cortex is estimated to contain 15–33 billion neurons, each connected by synapses to several thousand other neurons. These neurons communicate with one another by means of long protoplasmic fibers called axons, which carry trains of signal pulses called action potentials to distant parts of the brain or body targeting specific recipient cells..

Traditionally the cerebral cortex is divided into four sections, which are known as lobes :

english latin deutsch français
Frontal Lobe Lobus frontalis Stirnlappen lobe frontal
Parietal lobe Lobus parietalis Scheitellappen lobe pariétal
Temporal lobe Lobus temporalis Schläfenlappen lobe temporal
Occipital lobe Lobus occipitalis Hinterhauptlappen lobe occipital

The Terminologia Anatomica (TA), the international standard on human anatomic terminology, developed by the Federative Committee on Anatomical Terminology (FCAT) and the International Federation of Associations of Anatomists (IFAA), released in 1998, defines two additional lobes : The limbic lobe, associated to emotion and memory and the insular cortex, associated to pain and some other senses.

The frontal lobe is associated with reasoning, motor skills, higher level cognition, and expressive language. The parietal lobe is associated with processing tactile sensory information such as pressure, touch, and pain. The temporal lobe is the location of the primary auditory cortex, which is important for interpreting sounds and the language we hear. The hippocampus is also located in the temporal lobe, which is why this portion of the brain is heavily associated with the formation of memories. The occipital lobe is associated with interpreting visual stimuli and information. The primary visual cortex, which receives and interprets information from the retinas of the eyes, is located in the occipital lobe.

The cerebral cortex is also segmented in cortical areas which are functionally or anatomically defined. Some examples are listed below :

human brain areas

brain areas

The brainstem is comprised of the hindbrain (rhombencephalon) and midbrain. The hindbrain contains structures including medulla oblongata, the pons and the reticular formation.

The limbic system contains glands which help relay emotions. Many hormonal responses that the body generates are initiated in this area. The limbic system includes the amygdala, hippocampus, hypothalamus and thalamus.

Great progresses in the analysis which parts of the brain are involved in a particular mental process have been made in the last years with the functional magnetic resonance imaging (fMRI).

More informations about human brain parts and regions are available at the following links:

at Wikipedia :

other sources :

BioBlender visualization

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BioBlender is a software package built on the open-source 3D modeling software Blender. BioBlender version 1.0 for Windows and Linux was released on July 12, 2013. The first beta version of BioBlender (v 0.1) was presented in September 2010.

BioBlender

BioBlender

BioBlender is the result of a collaboration, driven by the SciVis group at the Institute of Clinical Physiology (CNR) in Pisa, Italy, between scientists of different disciplines (biology, chemistry, physics, computer sciences) and artists, using Blender in a rigorous but at the same time creative way.

With BioBlender users can handle proteins in the 3D space, displaying their surface in a photorealistic way, and elaborate protein movements on the basis of known conformations. Scientists all over the world study proteins at atomic level and deposit information in the public repository Protein Data Bank, where each molecule is described as the list of its atoms and their 3D coordinates.

BioBlender can be used for:

  • import and visualize Protein Data Bank (PDB) files (The PDB file format is a textual file format describing the three dimensional structures of molecules held in the Protein Data Bank)
  • simulate molecular dynamics and optimize protein motion
  • visualize complex protein surface properties  (e.g. MLP and EP surface properties)

A BioBlender tutorial was published by Raluca Andrei, Mike Chen Pan and Monica Zoppè, in the BlenderArt magazine N.31 in December 2010.

Biological and artificial neurons

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Biological neurons

A biological neuron (nerve cell) is an electrically excitable cell that processes and transmits information through electrical and chemical signals. A chemical signal occurs via a synapse, a specialized connection with other cells. Neurons connect to each other to form neural networks. Neurons are the core components of the nervous system, which includes the brain, spinal cord, and peripheral ganglia. There are different types of neurons: sensory neurons, motor neurons and interneurons.

A typical neuron possesses a soma (perkaryon or cyton = cell body with nucleus), dendrites and an axon. Neurons do not undergo cell division.

Neurons

Neuron (Wikipedia)

Dendrites are thin structures that arise from the cell body, branching multiple times and giving rise to a complex dendritic tree. An axon is a special cellular extension that arises from the cell body and travels for long distances (as far as 1 meter in humans). The cell body of a neuron gives rise to multiple dendrites, but never to more than one axon, although the axon may branch hundreds of times before it terminates. The axon terminal contains synapses, specialized structures where neurotransmitter chemicals are released to communicate with target neurons. At the majority of synapses, signals are sent from the axon of one neuron to a dendrite of another, however there are a lot of exceptions.

All neurons are electrically excitable, maintaining voltage gradients across their membranes by means of metabolically driven ion (sodium, potassium, chloride, calcium) pumps. Changes in the cross-membrane voltage can alter the function of voltage-dependent ion channels. Each time the electrical potential inside the soma reaches a certain threshold, an all-or-none electrochemical pulse called an action potential is fired, which travels rapidly along the cell’s axon, and activates synaptic connections with other cells when it arrives.

Artificial neurons

An artificial neuron is a mathematical function conceived as an abstraction of biological neurons. The artificial neuron receives one or more inputs (representing the dendrites) and sums them to produce an output (representing the axon). Usually the sums of each node are weighted, and the sum is passed through a non-linear function known as an activation function or transfer function.

The first artificial neuron was the Threshold Logic Unit (TLU) first proposed by Warren McCulloch and Walter Pitts in 1943. This model is still the standard of reference in the field of neural networks and called a McCulloch–Pitts neuron. However, artificial neurons of simple types, such as the McCulloch–Pitts model, are sometimes characterized as caricature models, in that they are intended to reflect one or more neurophysiological observations, but without regard to realism.

In the 1980s computer scientist Carver Mead, who is widely regarded as the father of neuromorphic computing, demonstrated that sub-threshold CMOS circuits behave in a similar way to the ion-channel proteins in cell membranes. Ion channels, which shuttle electrically charged sodium and potassium atoms into and out of cells, are responsible for creating action potentials. Using sub-threshold domains mimicks action potentials with little power consumption.

At the Neuromorphic Cognitive Systems Institute of Neuroinformatics of the University of Zurich and ETH Zurich, a research group leaded by Giacomo Indiveri is currently developing, using the sub-threshold-domain principle, neuromorphic chips that have hundreds of artificial neurons and thousands of synapses between those neurons.

Volunteer Computing

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Volunteer computing is an arrangement in which people (volunteers) provide computing resources to projects which use the resources to do distributed computing and/or storage. Distributed computing is a field of computer science that studies distributed systems. A distributed system is a software system in which components, located on networked computers, communicate and coordinate their actions by passing messages.

Neural networks are very good candidates for simulation by distributed computing systems because of their inherent parallelism and beacuse its simulation is a very time consuming process, due to the complex iterative process involved.

The first volunteer computing project was the Great Internet Mersenne Prime Search, which was started in January 1996. The term volunteer computing was coined by Luis F. G. Sarmenta, the developer of Bayanihan.

The Berkeley Open Infrastructure for Network Computing (BOINC) is the most widely-used middleware system for volunteer computing. It offers client software for Windows, Mac OS X, Linux, and other Unix variants. The project was founded at the University of California, Berkeley Space Sciences Laboratory, funded by the National Science Foundation. Other systems are XtremWeb,  Xgrid and Grid MP.

Volunteer computing systems must deal with the following problems, related to correctness :

  • Volunteers are unaccountable and essentially anonymous
  • Some volunteer computers occasionally malfunction and return incorrect results
  • Some volunteers intentionally return incorrect results or claim excessive credit for results

A list of distributed computing projects is provided at Wikipedia. Links to a few selected BOINC volunteer computing projects are listed below :