CHemoarchitectonic Atlas of the Mouse thalamus as a BNDU OpEn Resource

calcium binding proteins, sagittal, kms024_v1v4_64

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 regional boundaries as regions of interest (ROIs)
  • 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


September, 2018




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

At the top right, there are the indicator for the XY coordinates, the plus button to toggle intensity querying (currently unstable), the arrow button to reset the image rotation, and the double arrow button for full screen view.

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.

Setting tabSave, 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.


LUTsChannel 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 labels work as toggle switches to turn on and off the channels. 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.

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

You can show and hide each ROI (region of interest) separately by ticking or unticking the boxes on the left, or all the ROIs at once by ticking/unticking Show at the top.

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

Iinfo tabBy default, when you enter the CHAMBER using the links above, you'll find the side panel on the right. Click the Info tab and then click the URL link at Dataset property to jump to the web client page.






web client metadataThe right side panel of the web client page contains metadata for each image or dataset. The Key-Value Pairs hold detailed information about immunohistochemstry etc. Acquisition tab also holds some metadata originating at the time of acquisition.

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