Multimodality multidimensional image analysis of cortical and subcortical plasticity in the rat brain

Abstract

In this work, we developed and implemented a multimodality multidimensional imaging system which is capable of generating and displaying anatomical and functional images of selected structures and processes within a vertebrate's central nervous system (CNS). The functional images are generated from [14C]-2-deoxy-D-glucose (2DG) autoradiography whereas the anatomic images are derived from cytochrome oxidase (CO) histochemistry. This multi-modality imaging system has been used to study mechanisms underlying information processing in the rat brain. We have applied this technique to visualize and measure the plasticity (deformation) observed in the rat's whisker system due to neonatal lesioning of selected peripheral sensory organs. Application of this imaging system revealed detailed information about the shape, size, and directionality of selected cortical and subcortical structures. Previous 2-D imaging techniques were unable to deliver such holistic information. Another important issue addressed in this work is related to image registration problems. We developed an image registration technique which employs extrinsic fiduciary marks for alignment and is capable of registering images with subpixel accuracy. It uses the information from all available fiduciary marks to promote alignment of the sections and to avoid propagation of errors across a serial data set.

A simple setup for episcopic microtomy and a digital image processing workflow to acquire high-quality volume data and 3D surface models of small vertebrates

“…Our setup requires the virtual alignment of stacked images. Fiducial markers have been shown to be valuable for image stack registration and to overcome known alignment problems such as the "banana" problem (e.g., Toga and Arnicar 1985;Brändle 1989;Ford-Holevinski et al 1991;Humm et al 1995;Goldszal et al 1996;Streicher et al 1997;Rau et al 2013). Our results confirmed that the use of external markers can increase alignment quality.…”

Evaluation of registration strategies for multi-modality images of rat brain slices

“…• the slice-order-preferred (Goldszal et al 1996) and • the combined modality-and-slice-order-preferred (Humm et al 2003, Dubois et al 2007.…”

“…Two-dimensional imaging techniques such as autoradiography are generally amenable only to single-parameter image acquisition due to different tissue-sample preparation procedures. Nevertheless, to provide quasi-simultaneous imaging, adjacent brain slices are often imaged by different modalities (Goldszal et al 1996, Dehnhardt et al 2007. This results in interleaved stacks of multi-modality slices with different slice-to-slice image characteristics or, alternatively, multiple single-modality stacks of slices with different stackto-stack characteristics.…”

“…Computer-based methods use either extrinsic features like fiducial markers (Humm et al 1995) or intrinsic features like landmarks and contours (Krinidis et al 2003, Rangarajan et al 1997, Zhao et al 1993, principle axes (Toga andBanerjee 1993, Hess et al 1998) and image intensities (Dehnhardt et al 2007, Palm et al 2005, Pietrzyk et al 2002. Fiducial markers like needles (Goldszal et al 1996) destroy parts of the tissue and are, therefore, not taken into consideration. Landmarks, contours and principle axes are not adequate for our application because the slice's shape as well as intrinsic landmark structures varies considerably, depending on the morphology of the imaged brain part.…”

Piecewise affine registration of biological images for volume reconstruction

“…fiducial markers: The use of fiducial markers helps increase the reliability of the registration process (Ford-Holevinski et al, 1991;Goldszal et al, 1996Goldszal et al, , 1995Humm et al, 1995). In histology, physical markers (straight rigid needles for instance) can be inserted into the organ to be processed, prior to the slicing step.…”