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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".