Introduction to the Atlas

Publication Details


The zebra finch as a model system:

The zebra finch has become a popular model system for studying behavioral and neuronal mechanisms of sexual imprinting, visual information processing, and especially for studying various aspects of song learning and behavior. The song system in birds, and in particular in the zebra finch, has become not only a versatile model system for studying neurobiology in birds, but also for research in neurosciences in general, to investigate such diverse problems as communication, neural development, plasticity and learning as well as behavioral endocrinology, and motor control.

The revised avian brain nomenclature:

In 2004 a milestone was set when after a long period of an intensive debate, discussion and decision making, an international consortium of experts and leading neuroscientists in the fields of avian, mammalian, reptilian and fish neurobiology proposed a revised nomenclature for avian telencephalon and some related brainstem nuclei (Reiner et al., 2004). This was an important step recognizing the many findings of recent molecular, anatomical and physiological data, clearly showing that many areas in the avian brain are homologous to their counterparts in mammals. The new nomenclature will help towards a better understanding in communicating about structure and function of brain areas in mammals and birds.

Reasoning for setting up the stereotaxic atlas:

The stereotaxic atlas of the brain of the zebra finch originally was carried out at the University of Bielefeld (Germany) in the lab of Professor Bischof (Lehrstuhl Verhaltensforschung). A variety of resources available at that time when the atlas was made, helped to name brain nuclei, areas and laminae. Especially, a copy of another as yet unpublished zebra finch brain atlas, made by Eugene Akutagawa in the lab of Professor Konishi, helped to reduce uncertainties concerning the identification of neuronal structures. Our atlas of the zebra finch brain was specifically designed to locate visual nuclei and areas such as the Nucleus Rotundus and the Ectostriatum, now termed the Entopallial nucleus, because the nomenclature for avian brain structure has been revised (Reiner et al., 2004). Xerox copies of the original version of the stereotaxic atlas of the brain of the zebra finch with the old terminology have been around for many years in various laboratories that are particularly interested in the visual system of the zebra finch. But the atlas has become also very popular for those groups that are working in the song system of birds.

For whom the atlas is made:

The song system of birds as a model system has evolved tremendously over the past two to three decades. With the new nomenclature it became clear that the old Xerox copies needed to be replaced by a thoroughly revised version that is updated and incorporating new findings concerning song system nuclei. Henceforth, the stereotaxic atlas of the zebra finch brain is very helpful to locate nuclei of the song system. In particular for students or young investigators who are just starting to identify song system nuclei such as HVC or LMAN. Using 100 μm free floating thick vibratome sections weakly stained with Toluidineblue and Methyleneblue in buffer facilitates recognizing nuclei of interest even when using binocular optics.

Aim of this study:

To bring forward this atlas to a wide community in an official way and to substitute the Xerox copies that are outdated by now, the stereotaxic atlas of the zebra finch brain is now updated with the new terminology. It has been kept mostly in its original form using transparencies for locating the exact coordinates of brain nuclei, but changes were also made and nuclei were added to account for the enormous knowledge that has been evolved over the last decades.

Please note that some of the abbreviations in the revised nomenclature were kept in its original form, but the meaning has been changed accordingly. For example, the abbreviation "E" is still valid, but is now linked to the Entopallial nucleus. Other terms were renamed, such as LMD, that is now named LPS (Lamina pallio-subpallialis). For more information on the new nomenclature of avian brain nuclei, please refer to Reiner et al., 2004a, Reiner et al., 2004b, Farries 2004, Jarvis et al., 2005.

Construction of the Atlas

The material and methods for setting up the schematic drawings of the brain of the zebra finch in transverse and sagittal sections is given in the following in form of a descriptive list according to the original.







The schematic drawings are available in two planes: sagittal and transverse. Depending on the head holder used in the various laboratories, the schematic drawings (Figures 1, 2, and 3) can be easily adjusted to the plane of section by making use of the mmtransparencies. Each single schematic drawing has now been made available to be individually augmented and upgraded with specific landmarks of brain structures. Therefore, this atlas can be used for any special approach by individual groups working on brain structures of the zebra finch.

Figure 1

Figure 1

Schematic drawing of the orientation of the brain in relation to the beak holder

Figure 2

Figure 2

Schematic representation of the cutting plane in transverse sections

Figure 3

Figure 3

Schematic representation of the cutting plane in sagittal sections


1.1 Getting ready for making lesions

1) Pulling tungsten electrodes

2) Insulating the tip with Isonel

3) Heating up the electrode at 30° Celsius

1.2 Making two lesions at a one mm distance

1) Anesthetizing the animal with Equithesin

2) Opening the skull of the zebra finch brain

3) Clamping the electrodes into the apparatus

4) Setting the lesions by electric current

5) Closing the scalp incision with Mirabond

1.3 Perfusion (after 24 hours)

1) Deep Nembutal anesthesia

2) Opening the thorax

3) Intracardiac perfusion with 0.9% saline solution

4) Intracardiac perfusion with formalin-saline solution

5) Debraining

6) Transferring the brain into 30% sucrose in formalin (24 hs)


2.1 Preparations for cutting sections

1) Making 'Gatenby-slides' 24 hs ahead

2) Cooling down the freezing stage of the microtome

3) Making an ice cube on the stage

4) Mounting the brain onto the ice cube

5) Putting a cylinder of tape around the brain and filling up the space in between with 5% ethanol

2.2 Cutting and taking pictures

1) Cutting at 30 μm steps

2) Taking pictures of every 3rd section directly from the cut surface of the frozen brain

3) Storing the cut tissue in 10% formalin

4) Mounting the sections onto 'Gatenby-slides'

5) Drying the sections on a heating plate

2.3 Methods of staining sections

1) Fink-Heimer staining technique

2) Fink-Heimer without cresyl violet counter-stain

3) Cresyl violet stain

2.4 Storage of sections

1) Coverslipping with Kanadabalsam

2) Hardening of the slides

3) Storing the slides in a box


3.1 Preparatory drawings

1) Developing the black-and-white negatives

2) Making contour drawings of the brain sections on the negatives by using an optical projector

3) Then making contour drawings of the tissue sections on the slides by projecting them onto transparent paper with the aid of a camera lucida

4) Comparing the contours of the contour drawings of the negatives with those ones of the projected tissue sections

5) Numbering the contour drawings consecutively with regard to their distance of each other

6) Drawing in and identifying brain structures of individual brains stained by different staining techniques, respectively

7) Fine orientation and thoroughly investigation of the brain structure in the sagittal and transverse plane

3.2 mm-drawings

1) Transferring the contour drawings including brain nuclei and area onto graph paper

2) Adjusting the location of identified brain nuclei and area in horizontal and vertical sections

3) Examination of identified brain structure

4) Checking thoroughly identified structures in terms of their location in transverse and sagittal sections


We are very grateful to the invaluable comments and helpful notes of Prof. Anton Reiner. We are particularly thankful to him for carefully checking each plate presented and making specific suggestions and corrections and for sharing the enthusiasm with us for this project. We would also like to thank the many colleagues who took great care in locating specific area and nuclei in the zebra finch brain by providing additional detailed drawings, sketches and maps in their papers. These publications were very useful and instructive to us and are cited in the reference list. We would like to highlight in this context particularly the valuable contributions of Dr. Martin Wild in unraveling a multitude of connections in the zebra finch brain. Funds for the support of the current work came from the German Science Foundation grant Ni 266/3 (1,2).


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