CHemoarchitectonic Atlas of the Mouse thalamus as a BNDU opEn Resource

kms024_s11v4_064 L+1.24 mm

CHAMBER (CHemoarchitectonic Atlas of the Mouse thalamus as a BNDU opEn Resource) is a chemoarchitectonic atlas of mouse thalamus prepared by scientists at MRC BNDU as a community resource.

CHAMBER offers "Google Maps experience" to the anatomy of mouse brain, with a special interest on the thalamus, the relay centre to the neocortex. The word thalamus has its origin in Latin, and it was originated from Greek word thalamos (θάλαμος), which means "inner chamber".

You can:

  • Scroll
  • Zoom in and out
  • Rotate
  • Turn on and off channels
  • Change colours
  • Change the display range of brightness
  • Overlay text annotations of structural names
  • See the distributions and colocalizations of marker proteins

for a variety of immunohistochemical markers as well as traditional Nissl staining for delineation of brain regions, such as thalamic nuclei.

The initial release includes immunoreactivities to calcium binding proteins (calretinin, calbindin, and parvalbumin) and Nissl staining on sagittal planes.


The CHAMBER team:

Kouichi C. Nakamura, Ben Micklem, Giulio Spagnol, Naomi Berry, Andy Sharott, and Peter J. Magill


5 March 2019




How to use CHAMBER?

Just click the links in the Dataset section above to begin.

CHAMBER uses the open-source OMERO platform with OMERO.iviewer, developed by The Open Microscopy Environment.

  OMERO logo


You can navigate the images in CHAMBER quite intuitively.

  • Mouse wheels or two finger swipes, depending on devices, provide zoom in and out.

  • Dragging the window invokes scrolling.

  • If you hold Shift key while dragging, you can rotate the image.


Image navigation tools



In addition to the basic manipulations above, at the top of the iviewer window, you'll find these tool buttons as above.

The buttons at the top left are for zooming out, zooming in, original view, and pixel size view Zoom.

You can also specify the magnification by giving a percentage percent.

At the top right, there are the indicator for the XY coordinates with the plus button to toggle intensity querying (currently unstable) X and Y,

the arrow button to reset the image rotation up,

and the double arrow button for full screen view full screen.


We highly recommend to try the full screen view full screen, especially on a large screen!

By default, when you enter CHAMBER using the links above, you'll find the side panel on the right. Click the Setting tab for customizing how the images are displayed.

SettingsSave, Save to all: These buttons are disabled for public users.

Undo, Redo, Copy, Paste: You can Undo or Redo your action on Settings. Copy will copy the current settings to the clipboard and you can Paste it to other images.

Grayscale: If you tick this, only the current channel will be shown in grayscale.

Interpolate: This is checked by default. At above 1:1 pixel zoom, the display is interpolated so that you don't see pixellation.


Channel NameChannel names: The channel name is written over its pseudo colour on the left of the sliders. Hovering your cursor over the truncated text will make the full channel name appear. The colour-filled channel names work as toggle buttons to turn on and off each channel. By clicking the down arrows to their right, you can change the channel colors or lookup tables (LUTs). You can also invert the values of each LUTs.

Sliders and boxes: used to set the display range of each channel via black and white points.

Min/Max: Set the display range based on the minimum and maximum values in present each channel.

Full Range: sets the white and black point for each channel to minimum and maximum values possible in the image's.

Imported: uses the black and white point values set in the file before it was imported into OMERO.

User Settings: We provide a Default Contrast preset so you can always return to the original display settings (channel colours and display ranges) after making adjustments.

ROI tab1. Currently, you need to click the ROIs tab in the right side panel to show annotations (mostly the names of structures).

2. You can show and hide individual ROIs (region of interests) separately by ticking or unticking the boxes on the left side of the list.

3. Or show and hide all the ROIs at once by ticking/unticking the box next to Show at the top.

4. When you click an ROI on an image, that ROI will be shown on the list on the right.

Structural annotations and abbreviations used for kms024v1v4 dataset is a subset of those used in The Mouse Brain in Stereotaxic Coordinates Third Eidition by Keith B.J. Franklin and George Paxinos (Academic Press, 2007) with a few exceptions.

A full list of abbrevations will be added soon.

Stractural namesThe ROIs include two vertical yellow lines in case of parasagittal planes and they represent the bregma and interaural lines in terms of anterior-posterior axis.


Show more buttonBy default, when you enter the CHAMBER using the links above, you'll see the thumbnails of subset of other images in the same dataset on the left. But this is NOT the all of images in this dataset. In order to show more, you need to click the button below or above (indicated by red arrows in the image).

Hide panelClose to the bottom at the border between the lef or right side panel and the main panel with the tissue image, you'll see a small button with two horizontal triangles (red arrow). the button

You can hide the side panel by clicking this button. When the side panel is hidden, by clicking the button again you can show the panel again.

Info tabBy default, when you enter the CHAMBER using the links above, you'll find the side panel on the right.

1.Click the Info tab

2. Then click the URL link at "Dataset" property to jump to the web client page, where all the images are shown.





General tabThe right side panel of the web client page contains metadata for each image or dataset. On the General tab, the Key-Value Pairs hold detailed information about immunohistochemstry etc.












Tags tabThe Tags tab on the left side panel allows you to search images and datasets with specific tags.

Method 1

Right click the navigation window, and you'll see a context menu with an option "Save Viewpoint as PNG." Select this and save the image as it appears on the screen at the screen resolution.

Save image as PNG



Method 2

From the web client page, find the download icon at the General tab on the right side of the window.

Choose "Download..." and you can download the whole image at the full resolution as the OME.TIFF format.