Using an Optical Clearing Technique for Visualizing the Midbrain Cholinergic System in Mice
Bibliographic record
Abstract
The 3D visualization of the midbrain cholinergic system is key for understanding its function and its relationship with other brain areas. In preliminary experiments, our lab used an optical clearing technique, CLARITY, along with confocal microscopy, to image cholinergic cells and projections in up to 4 mm thick brain slices. Brains from transgenic mice expressing YFP under the choline aceteyltransferase 1 (CHaT1) promotor were harvested and sliced into coronal sections of different thicknesses. The samples were then embedded into a hydrogel monomer solution for 3 hours and left to incubate at 37°C. Afterwards, the tissue samples were left in a clearing solution for lipid membrane removal and left to incubate at 37 °C between 19 to 44 days.When qualitatively studied, passive CLARITY was found to effectively clear coronal sections of 1, 2, 3 and 4 mm thick after 19, 26, 35 and 44 days of incubation, respectively. Confocal microscopy confirmed sufficient expression of YFP to visualize thin axons and single axon terminals of cholinergic neurons within the rostral regions of the mouse brain. Based on our preliminary results, our ultimate goal is to construct a 3D visualization of the entire midbrain cholinergic system and its projections in the mouse brain.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.001 |
| Meta-epidemiology (narrow) | 0.002 | 0.002 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.003 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.004 |
| Insufficient payload (model declined to judge) | 0.005 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".