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enter image description here Why is the internal capsule dark in this transverse/horizontal section of the brain? If it is white matter, then why isn't it white?

P. S. : Formalin was used for fixation. Why the same color was not for remaining white matter.

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Short answer
White matter is called white matter because it is relatively white compared to gray matter. However, in fixated specimens it is not as snowy white as in textbook pictures.

Background
The internal capsule is a paired V-shaped structure that is visible in horizontal brain slices (Fig. 1). It is a subcortical structure mainly consisting of fiber tracts connecting the cortex to the brainstem.

brain slice
Fig. 1. Horizontal (transverse) brain slice showing internal capsule. source: Utah University

In Fig. 1 the structure is quite white'ish, but in the following two images you can see it is not always the case.

brain
source: The Human Brain: Chapter 5: The Cerebral Hemispheres

brain
Fig. 3. source: Medicos Notes

As you can see, the internal capsule is not always nice and white. Fig. 2 particularly shows a reddish taint of many white matter structures.

The internal capsule is well-vascularized (Schamann, 2003) and strokes in this region are associated with muscle weakness and loss in sensory sensitivity (source: Stanford Medicine). Hence, the red coloration may well be due to red blood cells that have not been completely washed out of the brain beore it was fixated. Also, non-specific coloring may happen over time in fixated specimens and many fixation artifacts can occur that lead to alterations in gross morphology (Chatterjee, 2014).

References
- Chatterjee, J Oral Maxillofac Pathol (2014); 18(S1): S111–6
- Schamann, Stroke (2003); 34: 2264-78

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  • $\begingroup$ That is fine and something that is obvious. Can you please be little more specific, why is it grayish (its not reddish)? What was effect of formalin on internal capsule and tapetum only, and not on remaining white matter? $\endgroup$ Mar 1, 2017 at 17:43
  • $\begingroup$ Hard to say, really. Was it formalin treated? How old is the prep? How often was it used? $\endgroup$
    – AliceD
    Mar 1, 2017 at 17:57
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    $\begingroup$ In aged fixed tissues, red blood cells appear much more brown than red, though I am not sure if that's a likely explanation here, I am not familiar with @AliceD's suggestion that the internal capsule is particularly vascularized. In general, the specimen pictured does not look like it is in great shape. There is very little color distinction between white and gray matter, for example. It's possible some of the change in coloration is simply because of the orientation of different fiber tracts and the resulting susceptibility to drying/aging, really more of a texture difference than color. $\endgroup$
    – Bryan Krause
    Mar 1, 2017 at 18:02
  • $\begingroup$ It was fixated in Jan 2016 using formalin. $\endgroup$ Mar 2, 2017 at 13:31
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    $\begingroup$ @AnubhavGoel I think it is typically thought to be better to preserve tissues long-term, especially brain, in ethanol rather than formalin (after intial fixation in formalin/paraformaldehyde). Long-term formalin storage can essentially "overfix" the tissue. I'm not certain that is what happened here, but without seeing the tissue before and around the initial fixation that's my best guess. $\endgroup$
    – Bryan Krause
    Mar 3, 2017 at 19:40

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