Written and maintained by CASRAI Editorial Board
Last updated
Reader task: understand what a Nissl stain shows, how it relates to cresyl violet, and what it cannot tell you, so you can choose it or a companion method for brain tissue.
Short answer
A Nissl stain uses basic dyes such as cresyl violet, thionine or toluidine blue that bind nucleic acids in cells. In neurons it colours the cytoplasmic Nissl substance (RNA-rich rough endoplasmic reticulum and ribosomes) and the nuclei, so it labels the whole neuronal population and reveals cell-dense layers of brain tissue.
What is Nissl stain?
Nissl staining is a histological method built on the interaction of basic dyes with the nucleic acid content of cells. A 2009 methods paper lists cresyl violet, thionine, toluidine blue, methylene blue and aniline dyes as examples. These dyes can bind DNA in nuclei but also the RNA concentrated in rough endoplasmic reticulum and ribosomes, which is the Nissl substance of the cytoplasm. The method is used to look at neuronal pathology and at the cytoarchitecture of brain areas, and it can serve as a counterstain after immunocytochemistry.
What do Nissl bodies indicate?
Nissl substance marks neuronal cell bodies. Because cell-dense regions take up more dye, a Nissl-stained cortical section shows dark, cell-rich layers (laminar structure) while white matter stays relatively unstained. That is why Nissl staining is described as a gold standard for cytoarchitecture in a 2013 comparison with optical coherence tomography.
Are Nissl granules found in nerve cells?
Yes. The Nissl substance (the granules or bodies seen after staining) is the RNA-rich rough endoplasmic reticulum and ribosomes in the cytoplasm of neurons, which is why neuronal cell bodies are the structures this stain highlights.
Cresyl violet vs Nissl staining
Nissl staining is the method; cresyl violet is one of the dyes used to carry it out. “Cresyl violet stain” and “Nissl stain” often describe the same bench result, but the Nissl class also includes thionine, toluidine blue, methylene blue and aniline dyes. Neutral red has also been used, with the difference that it was reported to label astrocytes as well.
What stain is used for neurons?
For labelling the whole neuronal population in tissue sections, a Nissl stain is the standard choice, because it stains neuronal cytoplasm without staining the perikarya of other brain cells in the same way. For single-cell shape, a Golgi stain is used instead; see Golgi stain. Brain staining methods therefore sort by question: how many cells and where (Nissl), what shape (Golgi), which protein (immunostaining).
Nissl vs Golgi: a sourced comparison
| Question | Nissl stain | Golgi stain |
|---|---|---|
| What it labels | Consistent labelling of the whole neuronal population | Neuronal morphology |
| Main strength | Cytoarchitecture, cell density, laminar organisation | Shape of individual neurons |
| Main limit | Very limited information on neuronal morphology | Does not give a whole-population readout |
Source for the table: a 2008 J Histochem Cytochem paper that combines Golgi and Nissl staining in one rapid method to study morphology and cytoarchitecture together.
What Nissl staining cannot tell you
- Soma size. In the same 2008 study, cresyl violet-labelled cell bodies appeared smaller at high cell densities, and the authors concluded that cresyl violet staining is inadequate for quantifying differences in soma size (examined in the dorsal cochlear nucleus). Counting and sizing designs are covered in stereology.
- Morphology. The stain gives very limited information on neuronal morphology; pair it with a method such as Golgi.
Practical pitfall: RNA loss after immunostaining
Because the stain depends on RNA, procedures that degrade RNA weaken it. The 2009 paper found that RNA degradation during immunocytochemistry lost cytoplasmic Nissl staining in rat sections (25 μm, freezing microtome), and that RNase-free conditions, with heparin used as an RNase inhibitor, preserved it. Teams combining Nissl with immunolabelling should plan for RNA protection from the start.
Where it matters for labs
Nissl-stained series are a common reference for locating regions and layers. In the 2013 optical coherence tomography study, free-floating sections were mounted on gelatin slides and every fifth section was stained, and the OCT images showed inverse contrast to Nissl. When tissue must be isolated after staining, see laser capture microdissection; for tissue viability rather than neuronal identity, see triphenyltetrazolium chloride.
Common misunderstandings
- “Nissl stain” and “cresyl violet” are not different techniques; one is the class, the other a dye.
- The distinctive Nissl signal is cytoplasmic Nissl substance, not only nuclei.
- It is a cell-body stain, not a fibre or morphology stain.
FAQ
What do Nissl bodies indicate?
Neuronal cell bodies: they are the RNA-rich rough endoplasmic reticulum and ribosomes of neuronal cytoplasm.
What stain is used for neurons?
Nissl stains such as cresyl violet label the neuronal population; Golgi stains show individual neuron shape.
What is the difference between cresyl violet and Nissl staining?
Nissl staining is the method; cresyl violet is one basic dye used in it, alongside thionine, toluidine blue and others.
Are Nissl granules found in nerve cells?
Yes, in the cytoplasm of neurons.
Sources (read 2026-11-07)
- Improved method for combination of immunocytochemistry and Nissl staining. J Neurosci Methods, 2009. PMC2753838, pmc.ncbi.nlm.nih.gov/articles/PMC2753838.
- A rapid method combining Golgi and Nissl staining to study neuronal morphology and cytoarchitecture. J Histochem Cytochem, 2008. PMC2386766, pmc.ncbi.nlm.nih.gov/articles/PMC2386766.
- Blockface histology with optical coherence tomography: a comparison with Nissl staining. NeuroImage, 2013. PMC4315235, pmc.ncbi.nlm.nih.gov/articles/PMC4315235.
