Hi Sophie Quick ,

It seems that you are going the right way! In histological assays of brains of rodent models of ischemia I also followed a well-established protocol mainly looking for evidence of time-related generation of proliferating Iba1+ microglia/macrophage and GFAP+ astrocytes in the penumbra after staining.

You may also look for Brdu+ and NeuN+ cells too in and IHC.

Although the aforementioned would suffice, you may take a look at the following paper for molecular markers from constituents of defective neurons and glial cells, cytokines, inflammatory acute-phase reactants, apoptosis, measurable alterations in oxidative stress and other miscellaneous molecular signs associated with stroke such as S100-β, Visinin-like protein 1, etc.

Article Maas MB, Furie KLMolecular biomarkers in stroke diagnosis an...

If you want measure and quantify apoptosis like an early changes In ischemia, Immunochemistry TUNEL or (Terminal deoxynucleotide transferase dUTP Nick End Labeling) is an assay to identify DNA fragmentation of apoptotic cells. TUNEL-positive cell represents apoptotic cell.

For example: Apoptotic and Necrotic Death Mechanisms Are Concomitantly Activated in the Same Cell After Cerebral Ischemia.

Isın U ̈ nal-C ̧ evik, MD, PhD; Munire Kılınc ̧, MD, PhD; Alp Can, MD; Yasemin Gu ̈ rsoy-O ̈ zdemir, MD, PhD; Turgay Dalkara, MD, PhD. In (Stroke. 2004;35:2189-2194.)

https://ahajournals.org/doi/pdf/10.1161/01.STR.0000136149.81831.c5