Monday, 3 of October of 2022

Links and References

Books, Journal Articles, and Websites

The following references are only a few of the excellent sources for information on animal anatomy, pathology, embryology, genetics, and study design that we have found of general help for the comparative pathology researcher. The list is by no means complete and will continue to be updated.

General Mouse and Rat Anatomy and Histology

Treuting PM and Dintzis SM. Comparative Anatomy and Histology: a mouse and human atlas. New York: Elsevier, 2012.

Constantinescu, GM. Duffee, N, Ed. Comparative Anatomy of the Mouse and the Rat: a color atlas and text. Memphis, American Association for Laboratory Animal Science (AALAS), 2011.

Cook, MJ. The Anatomy of the Mouse. Academic Press 1965. Adapted for the web by Mouse Genome Informatics, The Jackson Laboratory, 2005, revised 2008.

Revised guides for organ sampling and trimming in rats and mice.  A collection of trimming guidelines for rodent tissue.

Freezing samples for cryosectioning.  A video outlining a way to freeze samples in OCT for cryosectioning.


National Toxicology Program. Nonneoplastic lesion atlas: a guide for standardizing terminology in toxicologic pathology for rodents. With sections on hematopoietic system, hepatobiliary system, integumentary system, nervous system, and urinary system.

International Harmonization of Nomenclature and Diagnostic (INHAND) Criteria for Lesions in Rats and Mice.

Proliferative and Nonproliferative Lesions of the Rat and Mouse Mammary, Zymbal’s, Preputial, and Clitoral Glands

Proliferative and Nonproliferative Lesions of the Rat and Mouse Urinary System

Proliferative and Nonproliferative Lesions of the Rat and Mouse Central and Peripheral Nervous Systems

Proliferative and Nonproliferative Lesions of the Rat and Mouse Hepatobiliary System

International Harmonization of Nomenclature and Diagnostic Criteria (INHAND):
Proliferative and Nonproliferative Lesions of the Respiratory Tract of the Rat and Mouse.

A monograph on histomorphologic evaluation of lymphoid organs. Toxicologic Pathology, 2006; 34(5):407-698


Antal C, Teletin M, Wendling O, Dgheem M, Auwerx J, and Mark M. Tissue Collection for Systematic Phenotyping in the Mouse. In Current Protocols in Molecular Biology. 29A.4.1- 29 A.4.23. John Wiley and Sons, 2007. Published online in Wiley Interscience.

Parkinson CM, O’Brien A, Albers TM, Simon MA, Clifford CB, and Pritchett-Corning KR. Diagnostic necropsy and selected tissue and sample collection in rats and mice. J. Vis. Exp. (54), e2966, DOI : 10.3791/2966 (2011).

Mouse Embryology

Kaufman MH. The Atlas of Mouse Development, 2nd revised ed. New York: Elsevier, 1994.

Kaufman M, Nikitin AY, and Sundberg JP. Histologic Basis of Mouse Endocrine System Development: a comparative analysis. Boca Raton: CRC Press, 2010.

Papaioannou VE and Behringer RR. Early embryonic lethality in genetically engineered mice: diagnosis and phenotypic analysis. Vet Pathol. 2012; 49(1):64-70.

Ward JM, Elmore AS, and Foley JF. Pathology methods for the evaluation of embryonic and perinatal developmental defects and lethality in genetically engineered mice. Vet Pathol. 2012; 49(1): 71-84.

Savolainen SM, Foley JF, and Elmore SA. Histology atlas of the developing mouse heart with emphasis on E11.5 to E18.5. Toxicologic Pathology, 2009; 37(4):395-414.

Emouseatlas Edinburgh Mouse Atlas Project (EMAP). EMA (3D mouse embryonic histology atlas) and EMAG (e-mouse atlas of gene expression).

Interactive 3D Mouse Limb Anatomy Atlas Mouse limb anatomy at E14.5 from the MRC National Institute for Medical Research Council.

Caltech µMRI Atlas of Mouse Development 3D digital atlas of normal mouse development constructed from magnetic resonance image data. Download 6 six atlases of C57BL/6 mice at Theiler Stages 13, 21,23, 24, 25 and 26 and MRI data for an unlabeled ts19 embryo.

Phenotyping of Genetically Engineered Mice

The January 2012: 49(1) issue of Veterinary Pathology is a special focus issue devoted to phenotyping of genetically engineered mice and contains excellent overviews by comparative pathologists on the assessment of mouse phenotypes.  A few of the titles in this issue are:

Sellers RS. The gene or not the gene–that is the question: understanding the genetically engineered mouse phenotype. Vet Pathol 2012; 49(1) 5-15.

Zeiss CJ, Ward JM, and Allore HG. Designing phenotyping studies for genetically engineered mice. Vet Pathol 2012; 49(1): 24-31.

Influence of Background Strain on Phenotype Assessment

Brayton CF, Treuting PM, and Ward JM. Pathobiology of aging mice and GEM: background strains and experimental design. Vet Pathol 2012; 49(1):85-105.

Sellers RS, Clifford CB, Treuting PM and Brayton CF. Immunological variation between inbred laboratory mouse strains: points to consider in phenotyping genetically immunomodified mice. Vet Pathol 2012: 49(1):32-43.


Bolon B and Butt MT. Fundamental Neuropathology for Pathologists and  Toxicologists. Hoboken, New Jersey: John Wiley and Sons, Inc. 2011.


NIEHS list of IHC protocols for mouse and rat tissue

Ward JM and Rehg JE. Rodent immunohistochemistry: pitfalls and troubleshooting. Vet Pathol. 2014; 51:88.

Ramos-Vara, JA and Miller MA. When tissue antigens and antibodies get along: revisiting the technical aspects of immunohistochemistry—the red, brown, and blue technique. Vet Pathol. 2014; 51: 42

Mouse Strains

International Mouse Strain Resource