Instructions & Guidelines

Ordering via NUCORE

• NUCORE Online Ordering Instructions
• Place an order for MHPL Services

Sample Submission Instructions

Multi-Organ Submission Policy

A "multi-organ submission" refers to multiple tissue types and organs derived from a single experimental animal. Please read our Multi-Organ Submission Policy.

ISH/RNAscope Order Guidelines

MHPL Guidelines for In Situ Hybridization (ISH) and RNAscope Services

Intercampus Courier Label

Intercampus Courier Shipping Label

Validating Order Numbers

Download step-by-step instructions to validate your order at NUCORE.

MHPL Service Rates

Download the pricing for our services: MHPL Service Rates FY26 (effective Sept. 1, 2025, through Aug. 31, 2026)

Staging Mouse Embryos

Mouse embryos can be staged according to a variety of criteria, the most general of which are those described by Theiler in "The House Mouse: Atlas of Mouse Development" (Springer-Verlag, New York, 1989).

• Theiler Criteria for Staging Mouse Embryos
• Download Mouse Embryo Staging

Atlas of Mouse Development

The following eMouseAtlas provides free access to high-resolution color images digitized from the original histological sections used by Kaufman for the Atlas of Mouse Development (1994).

Histology Atlas of the Mouse Placenta

The following paper provides an overview of histological transformations during the development of the mouse placenta which can be useful in identifying and describing changes in engineered, induced, and spontaneous disease models.

• Histology Atlas of Mouse Placental Development
• Download Atlas of Placental Histology

Histology Atlas of Mouse Urinary System Development

This review focuses on the histology of the mouse urinary system during embryonic development.

• Atlas of Mouse Embryonic Development of the Urinary System
• Download Urinary System Development Histology Atlas

Histology Atlas of Mouse Heart Development

• Atlas of Mouse Embryonic Heart Development
• Download Embryonic Heart Development Histology Atlas

Histology of Mouse Lung Development

Histology Atlas of Liver Development

• Histology Atlas of Mouse Embryonic Liver Development
• Download Atlas of Mouse Liver Development

Brain Atlases

The Allen Brain Map is an excellent resource in neuroscience research and includes neuroanatomical atlases for mouse CNS, and human brain across multiple developmental timepoints.

Anatomy & Histology of the Pancreas

Non-Neoplastic Lesion Atlas

The Non-Neoplastic Lesion Atlas hosted by the National Toxicology Program is a guide for standardizing toxicologic pathology in rodents. The atlas is subdivided into chapters covering a single organ. See the Non-neoplastic lesion atlas.

Sampling of Rodent Organs for Histology

The following papers summarize suggested guidelines for preparing various organs in tissues from rodents for histological analysis.

• Tissue Collection for Systematic Mouse Phenotyping
• Respiratory, Reproductive and Thymic Organs
• Neuronal, Urogenital Tract, Cardiovascular, and Immune Organs

Intestinal Swiss Rolls

• Download the detailed JOVE protocol for preparing intestinal Swiss rolls
• Watch the video to prepare intestinal Swiss rolls for histology

Fixation of Lungs for Histology

• Tracheal Perfusion with Fixative
• Lung Air-Inflation Vascular Perfusion-Fixation

Transcardial Perfusion-Fixation

This method is the preferred fixation strategy for CNS tissues and also to flush out blood from organs: Intracardiac Perfusion-Fixation.

Glyoxal Fixation

Glyoxal can replace formaldehyde-based fixatives (10% NBF or 4% PFA) as a fast-acting cross-linker that also preserves protein and nucleic acid antigenicity. Glyoxal-fixation typically results in brighter microscopy images. Get the Glyoxal Fixation Protocol.

Lipid Fixation with Chromic Acid

Chromic acid can fix lipids in tissues prior to creation of FFPE blocks. This is a convenient alternative to cryosections for evaluation of lipid accumulation: Chromic Acid Fixation of Lipids for FFPE.

Fixation of Ocular & Testicular Specimens

• Davidson's Fixative for Eyes and Testes
• Recipe for Modified Davidson's Fixative

Heart Tissue Processing for Infarct Analysis

This protocol describes the use of a tissue matrix to sample thick sections of the heart for a systematic survey of myocardial infarct: Histological Analysis of Myocardial Infarct.

Decalcification With Immunocal

This method is a formic acid-method using Immunocal for decalcifying mineralized tissues to make them suitable for microtomy and subsequent histology and immunostainings. Download the decalcification with Immnocal protocol.

Decalcification With EDTA

This method for decalcification utilizes a buffered EDTA-sucrose solution. This method is suitable for spatial transcriptomics to maintain the integrity of RNA in the tissues: Download the decalcification with EDTA protocol.

Rotary Microtome Self-Service Guidelines

Microm HM325 Microtome Manual

Paraffin Microtomy Tips & Additional Resources

Download the following useful resource on paraffin microtomy from Leica: Microtomy & Paraffin Section Preparation.

Cryostat User Guidelines

MHPL Cryostat User Guidelines

Dakewe CT520 Cryostat Manual & Instructional Video

• Dakewe CT520 User Manual (Full)
• Dakewe CT520 Quick Reference Manual
• Watch the Instructional Video

OCT Embedding

Cryosectioning Tutorial

Vibratome Self-Service Policies

Leica VT1200S User Manual

Vibratome Sectioning of Rodent Brain Slices

• Mouse Brain Sectioning with the Vibratome (VIdeo Tutorial)
• Rat Brain Sectioning with the Vibratome

Sectioning of Thick Liver Slices

Optimization of Vibratome Sectioning

Histogel Embedding

Alginate Embedding

Prepare Slides of Single Cell Suspensions

The Cytospin method prepares single cell suspension smears on glass slides by centrifugation suitable for downstream histology, immunostaining or nucleic acid in situ hybridization.

Multiplex Fluorescent RNAscope

miRNAscope & RNAscope Plus Assays

• miRNAscope HD-Red Assay (Chromogenic/Fluorescent)
• RNAscope Plus (RNAscope and small RNA co-detections-Fluorescent)

RNAscope for Cultured Cells

DNAscope Duplex (Chromogenic)

X-CLARITY Tissue Clearing

X-CLARITY Tissue Clearing Protocol

MHPL Guidelines for X-CLARITY System Self-Service

Selection of Antibodies

CITEAB is a useful website summarizing applications and published citations for commercially available antibodies.

Selecting Positive Control Tissues

Here are useful resources for identifying positive control tissues for immunolabelings and in situ hybridization:

• NCBI Gene
• Human Protein Atlas
• Cell Marker

Fiji/ImageJ

FIJI/ImageJ is a widely used, free and open-source software platform for scientific image analysis.

QuPATH

QuPATH is an open-source, cross-platform software application primarily used for bioimage analysis, particularly within the context of digital pathology and whole slide image analysis.

CellProfiler

CellProfiler is a free, open-source image analysis software designed for biologists to automatically identify, quantify, and analyze biological entities in images. It allows users to create custom pipelines using various image processing and object analysis modules, facilitating reproducible and quantitative analysis of cell and subcellular features.

RNAscope Data Analysis

This ACD web resource provides a wealth of information on how to analyze RNAscope data in chromogenic singleplex/duplex to multiplex fluorescent scenarios.

CellProfiler Analysis of RNAscope & BASEscope Data

This ACD web resource provides instructions on how to analyze RNAscope or BASEscope results using CellProfiler. Learn to Analyze RNAscope/BASEscope Data Using CellProfiler.

PIXIMI

Piximi is an open-source, browser-based platform for interactive bioimage analysis. Designed for accessibility and flexibility, Piximi enables users to perform advanced image processing tasks without requiring any installation or deep machine learning expertise. Built with researchers and biologists in mind, it provides a user-friendly interface for annotation, segmentation, classification, and quantitative measurement of microscopy images.

3D Printing Brain Matrices

This protocol provides instructions on how to 3D print mouse brain slicing matrices: Custom Mouse Brain Matrix.

3D Printing Services are available at:

• MakerLab at the Mudd Library in the Evanston campus
• CAM/NIC at Searle Building on the Chicago campus

3D Printing of Tissue Sectioning Matrix

3D Printing Services are available at:

• MakerLab at the Mudd Library in the Evanston campus
• CAM/NIC at Searle Building on the Chicago campus

Thick Slicing of Brain & Heart Using a Tissue Matrix

This instructional video shows how to systematically slice thick sections of brain and heart tissues using a tissue matrix.