Biology subjects

Gerin-Lajoie, A.

Publications and source records attributed to Gerin-Lajoie, A..

6 recordsLinked to original sources

bioRxiv2026

Neuronal quantification in the primary motor cortex of mouse brains fixed with solutions from human gross anatomy laboratories

Background: Brain banks usually provide small tissue blocks fixed by immersion in neutral-buffered formalin (NBF). While still underexploited for research, gross anatomy laboratories could provide full brains fixed by perfusion with solutions better suited for gross anatomy dissection. However, the chemicals in these solutions might have a different impact on histology protocols for cell quantification than in NBF-fixed brains. The main goal of this study is to compare the effects on the number and size of labeled neurons of the primary motor cortex (PMC) of mouse brains fixed with three different solutions: (1) NBF, typical of brain banks, (2) a saturated salt solution (SSS), and (3) an alcohol-formaldehyde solution (AFS), both used in human anatomy laboratories. Methods: 27 C57BL/6J mouse brains were perfused with the NBF (N=9), SSS (N=9) or AFS (N=9), then cut in 40-m slices and processed with immunohistochemistry to target neurons. Various quantitative variables were assessed manually and automatically on photomicrographs of 3 regions of interest (ROIs) of the PMC per specimen, namely the total and individual neuronal profile areas, number and diameters. The effects of the three fixatives on these variables were compared using ANOVA or Kruskal-Wallis, depending on the distribution. For measures on individual cells, a generalized linear mixed model was applied. Dice coefficients and correlations were applied to evaluate the agreement of the manual and automatic methods. Results: There was no significant difference between the brains fixed by the three fixatives for the total and individual cell areas, the total cell count and the cell diameters. The values obtained from manual and automatic measures had an overall good agreement (Dice coefficients > 0.79). Conclusion: It was found that the SSS and AFS had similar impacts on the quantitative variables in the tissue as the NBF. These results are promising for neuroscientists interested in using brains from anatomy laboratories for quantitative research on neurons from the PMC.

neuroscience↗

bioRxiv2026

Immunofluorescence quality of human brain tissue fixed with solutions used in gross anatomy laboratories

Brain banks provide small tissue samples fixed in neutral-buffered-formalin (NBF), but human anatomy teaching laboratories could provide full brains fixed with solutions that are more appropriate for gross anatomy such as a saturated salt solution (SSS) or an alcohol-formaldehyde solution (AFS). Advanced aging and prolonged exposure to aldehydes are known to enhance brain tissue autofluorescence (AF), limiting the efficacy of immunofluorescence (IF) procedures. We have previously shown by IF staining the antigenicity preservation in mouse brains fixed with the three solutions. We now aimed to compare the quality of IF staining in human brains fixed with SSS, AFS and NBF. In addition, we compared the efficiency of AF quenching methods, namely the application of SudanBlackB (SBB) and the treatment of sections with sodium borohydride (NaBH4). Blocks of neocortex were extracted from 18 brains (NBF=6, SSS=6, AFS=6) and cut into 40{micro}m sections. Neurons (anti-NeuN, AlexaFluor-488) and astrocytes (anti-GFAP, AlexaFluor-555) were revealed with IF after an antigen retrieval protocol, while two treatments (SBB or NaBH4) were used to quench AF. We then assessed the degree of AF (criteria: background or cell AF) and the immunostaining quality with excitation wavelengths of 488nm, 555nm and 647nm. Brains fixed with all three solutions showed well-labeled astrocytes, whereas neurons werent always stained, but this was not associated to the fixative solution. The overall AF intensity was similar in sections from brains fixed with all three solutions. Finally, the SBB treatment was the most effective at reducing AF in all specimens. Given the similarity in AF and antigenicity assessment across the three solutions, we conclude that brains fixed with SSS and AFS could be good alternatives for NBF-fixed specimens in the context of IF experiments processed with a SBB protocol. Highlights- Immunofluorescence staining is feasible in brains fixed with anatomy labs solutions - GFAP is less affected by fixation than NeuN - Autofluorescence can be reduced by Sudan Black treatment

neuroscience↗

bioRxiv2025

Comparison of T1- and T2-weighted MRI contrasts of ex vivo ex situ brains fixed with solutions used in gross anatomy laboratories

Post-mortem magnetic resonance imaging (MRI) offers high resolution and histological correlation, so protocols have been developed by brain banks using hemispheres fixed by immersion in Neutral-buffered formalin (NBF), but they provide limited tissue samples. Conversely, anatomy laboratories could supply complete brains perfused either with a salt-saturated (SSS) or an alcohol-formaldehyde (AFS) solution. These fixation methods alter the brains molecular properties, potentially affecting MRI quality and structural characteristics. T1- and T2-weighted (T1w, T2w) contrasts change with NBF fixation, but the effects of SSS or AFS remain unknown. We compared T1w and T2w intensities of different regions of interest (ROIs), including subcortical white matter (WM), cortical and deep gray matter (GM), in brains fixed with NBF, SSS and AFS. We scanned 20 ex situ hemispheres (NBF-immersed=7; SSS-perfused=7; AFS-perfused=6) in a 3T MRI scanner using T1w (0.7mm3) and T2w (0.64mm3) sequences overnight. Mean intensities of 29 ROIs in T1w and T2w MRIs and GM-WM ratios were calculated and compared in brains fixed with the three solutions. We found that T1w images were more affected by the fixation process, inverting the contrast of in vivo T1w and reducing the GM-WM contrast in AFS-fixed brains. T2w images resembled in vivo scans and maintained a sharp contrast in brains fixed with the three solutions, although the GM-WM intensity ratios were lowered in SSS-fixed brains. In conclusion, brains fixed with SSS and AFS from anatomy laboratories could be used for MRI studies, especially with the T2w sequence that seems more appropriate for structural analyses in different ROIs.

neuroscience↗

bioRxiv2025

Histology to MRI registration quality of ex vivo human brain blocks fixed with solutions used in anatomy laboratories

IntroductionPost-mortem brain tissue is obtained from brain banks that provide small tissue samples, while gross anatomy laboratories could become a source of complete brains for neuroscientists. These are preserved with solutions whose chemical composition differs from the classic neutral-buffered formalin (NBF) used in brain banks, such as a saturated-salt-solution (SSS) or an alcohol-formaldehyde solution (AFS) that preserve antigenicity of the main brain cell populations. Since histology remains the gold standard in neuroscientific research, while MRI is the most common imaging modality, MRI-histology registration quality needs to be assessed to ensure the suitability using brains fixed with innovative solutions for research procedures. Hence, our goal was to compare the registration quality of human brains fixed with NBF, SSS and AFS, as well as the histological characteristics that could affect the registration. MethodsWe used 12 human brain blocks of 3x3x3 cm3 fixed in our anatomy laboratory using SSS (N=4), AFS (N=4), or NBF (N=4). The blocks were scanned using a 7Tesla Bruker animal MRI scanner with a T2-TurboRARE sequence at 0.13x0.13x0.5mm3. Blocks were then cut into 40m thick sections (parallel to the 0.13x0.13 plane) using a vibratome. Sections were stained with histochemistry (HC) (Cresyl violet, Prussian blue, Luxol fast blue, H&E, and Bielschowsky) and immunohistochemistry (IHC) of the 4 main cell populations: neurons (NeuN), astrocytes (GFAP), microglia (Iba1) and myelin (PLP) either with or without an antigen retrieval (AR) protocol. Stained sections were imaged using a slide scanner microscope and segmented with masks using Display, and the sections were manually registered to the T2-TurboRare images using landmarks in Register (MincToolKit). ResultsMore landmarks were needed to achieve proper alignment of the histology to MRI images for the SSS-fixed blocks, due to the lower GM-WM contrast in these brains. However, there was no significant difference in the staining intensity of the histology sections of blocks fixed with the three solutions, while SSS-fixed blocks showed a lower percentage of overlap between the good histology quality masks and the MRI masks. This resulted in a sufficient registration quality of all blocks, although more challenging when fixed with SSS. ConclusionWe have developed histology, MRI and registration protocols that are of good quality in brain blocks fixed with solutions used in gross anatomy laboratories. These results are promising for neuroscientists interested in using full brains from anatomy laboratories, either using MRI, histology or registration of both modalities to study normal aging and neurodegenerative conditions.

neuroscience↗

bioRxiv2025

Ex vivo human brain volumetry: validation of magnetic resonance imaging measurements

BackgroundNeurodegenerative diseases are associated with brain atrophy. The volume of in vivo human brains is determined with various magnetic resonance imaging (MRI) measurement tools of which the validity has not been assessed against a gold standard. Here, we propose to validate the MRI brain volumes by scanning ex vivo-in situ specimens (i.e., anatomical heads), which allows the extraction of the brain after the scan to compare its volume with the gold standard water displacement method (WDM). MethodsWe acquired 3T MRI T2-weighted, T1-weighted, and MP2RAGE images of seven anatomical heads fixed with an alcohol-formaldehyde solution routinely used in anatomy laboratories and segmented the gray and white matter of the brain using two methods: 1) a manual intensity-based threshold segmentation using Display (MINC-ToolKit, McConnell BIC), and 2) an automatic Deep-Learning-based segmentation tool (SynthSeg). The brains were then extracted, and their volumes were measured with the WDM after the removal of their meninges and a midsagittal cut (to allow water penetration into the ventricles). Volumes from all methods were compared to the ground truth (WDM volumes) using a repeated-measures ANOVA. ResultsMean brain volumes, in cubic centimeters, were 1111.14{+/-}121.78 for WDM, 1020.29{+/-}70.01 for manual T2-weighted, 1056.29{+/-}90.54 for automatic T2-weighted, 1094.69{+/-}100.51 for automatic T1-weighted, 1066.56{+/-}96.52 for automatic MP2RAGE INV1, and 1156.18{+/-}121.87 for MP2RAGE INV2. All volumetry methods were significantly different (F=17.874; p<0.001) from the WDM volumes, except the automatic T1-weighted volumes. ConclusionWe demonstrate that SynthSeg accurately determines the brain volume in ex vivo-in situ T1-weighted MRI scans. Our results also suggest that given the contrast similarity between our ex vivo and in vivo sequences, the brain volumes of clinical studies are most probably sufficiently accurate, with some degree of underestimation depending on the sequence used.

neuroscience↗

bioRxiv2024

Comparison of histological procedures and antigenicity of human post-mortem brains fixed with solutions used in gross anatomy laboratories

BackgroundBrain banks provide small tissue samples to researchers, while gross anatomy laboratories could provide larger samples, including complete brains to neuroscientists. However, they are preserved with solutions appropriate for gross-dissection, different from the classic neutral-buffered formalin (NBF) used in brain banks. Our previous work in mice showed that two gross-anatomy laboratory solutions, a saturated-salt-solution (SSS) and an alcohol-formaldehyde-solution (AFS), preserve antigenicity of the main cellular markers. Our goal is now to compare the quality of histology and antigenicity preservation of human brains fixed with NBF by immersion (practice of brain banks) vs. those fixed with a SSS and an AFS by whole body perfusion, practice of gross-anatomy laboratories. MethodsWe used a convenience sample of 42 brains (31 males, 11 females; 25-90 years old) fixed with NBF (N=12), SSS (N=13), and AFS (N=17). One cm3 tissue blocks were cut, cryoprotected, frozen and sliced into 40 m sections. The four cell populations were labeled using immunohistochemistry (neuronal-nuclei (NeuN), glial-fibrillary-acidic-protein (GFAP), ionized-calcium-binding-adaptor-molecule1 (Iba1) and myelin-proteolipid-protein (PLP)). We qualitatively assessed antigenicity and cell distribution, and compared the ease of manipulation of the sections, the microscopic tissue quality, and the quality of common histochemical stains (e.g., Cresyl violet, Luxol fast blue, etc.) across solutions. ResultsSections of SSS-fixed brains were more difficult to manipulate and showed poorer tissue quality than those from brains fixed with the other solutions. The four antigens were preserved, and cell labeling was more often homogenous in AFS-fixed specimens. NeuN and GFAP were not always present in the NBF and SSS samples. Some antigens were heterogeneously distributed in some specimens, independently of the fixative, but an antigen retrieval protocol successfully recovered them. Finally, the histochemical stains were of sufficient quality regardless of the fixative, although neurons were more often paler in SSS-fixed specimens. ConclusionAntigenicity was preserved in human brains fixed with solutions used in human gross-anatomy (albeit the poorer quality of SSS-fixed specimens). For some specific variables, histology quality was superior in AFS-fixed brains. Furthermore, we show the feasibility of frequently used histochemical stains. These results are promising for neuroscientists interested in using brain specimens from anatomy laboratories.

neuroscience↗