Figure 1.
Diagrams of axonal tracing paradigm and connections of rat brain somatosensory cortex.
(A) Schematic diagram showing the principles of anterograde axonal tracing. Following injection of an anterograde axonal tracer to a brain region (I), the tracer is taken up by neurons (red dot in region I) within the injection site, and anterogradely transported along efferent axons, yielding distinctly labeled axons and terminal fields (solid lines) in regions (II, III) receiving axonal projections from the injected region. While the tracer Phaseolus vulgaris leucoagglutinin only gives anterograde labeling (solid red lines), the bidirectional tracer biotinylated dextran amine, also gives rise to retrograde labeling of neurons (red dot in region II), as well as secondary anterograde labeling of collateral axons (dashed red lines to regions II and IV). (B) Diagram of the rat brain showing axonal projections from the primary somatosensory cortex to well-known ipsilateral (solid red lines) and contralateral (dashed red lines) subcortical targets. (C) Schematic wiring diagram (modified from [31]) showing the input and output relationships of the primary somatosensory cortex (SI). SI input from the trigeminal system is shown (solid black lines). SI output connections (solid red lines) reach several cortical and subcortical regions. Grey shading indicates regions investigated in the present study (Fig. 5). CP, caudate putamen; Cb, cerebellum; MI, primary motor cortex; PN, pontine nuclei; Po, posterior complex thalamus, PR, perirhinal cortex; Rt, reticular nucleus thalamus; SI, primary somatosensory cortex; SII, secondary somatosensory cortex; SC, superior colliculus; TN, trigeminal nuclei; VB, ventrobasal complex thalamus.
Figure 2.
(A) Flowchart showing four processing steps, beginning with an animal submitted to an axonal tract-tracing experiment, followed by tissue and image processing steps, to an end result consisting of section images in a database. For each step, information about experimental parameters and procedures (metadata) are stored together with the section images. (B) Diagram showing module details and the input and output elements of each module in the workflow.
Figure 3.
Formalized overview of experimental metadata recorded for axonal tracing experiments.
Information deemed necessary for the interpretation and re-use of axonal tracing experiments, sorted according to the processing steps shown in Figure 2.
Figure 4.
Graphical user interface of the online image repository.
(A) Viewer tool providing access to a series of images organized by bregma levels. Thumbnail images (bottom row) provide overview of the available images, and selected images can be explored in the viewer panel by interactive zooming and panning. Metadata are available via a link in the viewer. (B–D) Evaluation of injection site location. Comparison of a BDA labeled section through the injection site (B) and a neighboring section (C) showing the SI barrel architecture (cytochrome oxidase staining). (D) Overlay of (B) and (C). Arrows indicate individual cytochrome oxidase positive SI whisker barrels.
Figure 5.
Overview of subcortical projections from SI whisker and forelimb representations.
Analysis of subcortical projections in six experiments with tracer injections in SI whisker or forelimb representations (row 1). Images are sorted according to animals (columns) and location (rows). Comparison within rows 2–6 demonstrates that projections from SI whisker and SI forelimb representations, respectively, have similar axonal distributions. Comparison within columns demonstrates considerable variability in the amount of labeled axons present in the different regions receiving SI projections. The bottom panels (A–I) show morphological details from regions indicated by frames in the superior colliculus (row 5) and trigeminal nuclei (row 6). Panels A′–I′ show processed images with background staining removed to facilitate visualization of labeled fibers. CP, caudate putamen; PN, pontine nuclei; Po, posterior complex thalamus, Rt, reticular nucleus thalamus; SI, primary somatosensory cortex; SC, superior colliculus; TN, trigeminal nuclei; VB, ventrobasal complex thalamus. Scale bars, 1 mm (rows 1–6) and 100 µm (A–I).
Figure 6.
Topography of corticothalamic projections from different body part representations in primary somatosensory cortex (SI).
(A–C) Images from corresponding locations in the thalamus from three experiments, showing labeled corticothalamic axonal plexuses. Inset figures indicate the localization and extent of injection sites. (D, F) Semitransparent overlays of image panels A and B, and B and C, showing distinct topographical distribution patterns in full agreement with earlier results from dual-tracing experiments. (E) Computerized plots showing topographical distribution of corticothalamic projections following SI tracer injections, modified from [51] and [50]. Scale bar: 1 mm.