Mouse Brain Library
Procedures & Protocols
Tissue processing · Imaging · Calibration · Software · Tutorials
Specimen Workflow
From Brain to Archive — Step by Step
01
Brain Extraction & Fixation
Brains are extracted under standard surgical protocol and immersion-fixed in formalin. Cases are prepared from genetically characterized inbred strains of mice.
02
12% Celloidin Embedding
Tissue is dehydrated and embedded in 12% celloidin solution. This embedding medium provides excellent section quality and dimensional stability for long-term archiving.
03
Microtome Sectioning — 30 µm
Embedded brains are cut at 30 µm thickness with a sliding microtome in either the coronal or horizontal plane. Typically 1-in-10 series are collected, giving 150 µm intervals between sections.
04
Cresyl Violet Staining
Sections are stained with cresyl violet (Nissl stain), an aniline dye that preferentially stains RNA and DNA, highlighting neuronal cell bodies, nuclei, and overall cytoarchitecture.
05
Slide Mounting & Coverslipping
Stained sections are mounted on glass slides and coverslipped. Four slides are prepared for every case; images of two of these four slides are made available online.
06
High-Resolution Imaging & Calibration
Slides are digitized at 24.5 ± 0.5 µm per pixel base resolution (3,060 × 2,036 pixels). Higher resolution imaging at 4.5 µm/pixel and 1 µm/pixel is performed for selected cases. Each image is calibrated using stage micrometer measurements.
07
Online Archive & Database Entry
Images and associated metadata (strain, age, sex, body weight, brain weight, cutting plane) are entered into the MBL database and made available through the online Brain Library Search.
Tutorials & Manuals
Reference Manual
MBL Training Manual — Detailed Protocol
The complete Mouse Brain Library Training Manual. This manual explains the full
process of embedding brain tissue in 12% celloidin, cutting the tissue with a
microtome, staining and coverslipping the brain sections, and posting images
on the internet for research purposes.
Open Training Manual
Atlas Creation
Mouse Brain Atlas Tutorial
Information, images, and HTML instructions for creating a labeled brain atlas
of your own. Covers section selection, annotation, web formatting, and
publication-ready presentation of neuroanatomical data.
View Atlas Tutorial
Imaging Procedure
Micrograph Imaging Tutorial
Step-by-step procedure used to scan the micrographs and acquire the data
available on this site. Covers electron microscopy imaging, scanner settings,
and the workflow for optic nerve micrograph sets.
View Micrograph Tutorial
Database Setup
MBL Slide Library Tutorial
Step-by-step instructions for creating your own slide database in FileMaker.
This tutorial covers data entry, image linking, search interface configuration,
and publishing the database on your own web server.
View Slide Library Tutorial
Microscope Software
iScope Internals Manual
A tutorial on the iScope internet microscope system. Covers the internal
architecture of the system, hardware requirements, and software configuration
for setting up remote microscopy.
Read iScope Manual
Software & Tools
Cell Counting · Macintosh
VideoScribbler for Mac
A program for the Macintosh that lets you draw on top of a live video source.
VideoScribbler was developed specifically for cell counting workflows.
Learn More
Stereology · Object Image
Point Counting Macros
A set of time-saving point counting macros for Object Image.
Automates the stereological grid overlay and counting workflow.
Download Macros
Free Image Analysis
ImageJ / NIH Image
A free, open-source image analysis platform based on NIH Image. Recommended
for opening and analyzing the JPEG images from the MBL at full quality.
Download ImageJ
iScope Client Suite
Gumbo + Aria3D Client
The integrated iScope client featuring Gumbo (stage control) and Aria3D
(3D visualization). Available for Mac OS X, Windows, and UNIX/Linux.
Register & Download
Technical Procedures
Histology
Tissue Processing Procedure
Detailed information on our tissue processing procedure — from brain
extraction through fixation, dehydration, celloidin infiltration,
embedding, and sectioning.
Read Tissue Protocol
Imaging & Calibration
Imaging Techniques and Calibration Procedures
Methods of image acquisition and calibration. Covers camera settings,
lens selection, stage micrometer calibration, pixel size verification,
and the imaging pipeline from microscope to archive.
Read Imaging Protocol
Image Viewing Notes
The quality of images displayed on your monitor will depend on your system, monitor settings, and other software configurations. To achieve best quality, save JPEG images locally and open them in ImageJ, NIH Image for Macintosh, Scion Image, or Photoshop.
Please use an up-to-date browser with at least 12 MB of memory allocated to your browser application. If images appear heavily pixelated or lack grayscale tone, your browser may be low on memory.