Jun 16, 2022

Advances in neuro-histology have necessitated the development of methods for quantifying large amounts of histology data and registering this data to standardized atlases in border defined structures for comprehensive data integration. As the field has accelerated to include large amounts of data to quantify, automation is becoming more important. Thus, Kristoffer Lauridsen and colleagues at the University of Colorado have developed a tool for Slice Histology Alignment, Registration, and Cell Quantification (SHARCQ).

Hand drawing borders to delineate brain regions is a labour intensive process. SHARCQ uses user-selected landmark points to warp images to a specified atlas that overlays the border for you. SHARCQ has several features such as adjustable atlas tilt to match out-of-plane histology, cell count registration that allows for import of cell counts from other counting files, interactive cell counts that allow for manual correction of cell location, 3D wire frame rendering capable of multi-cell-type visualization, multi-atlas integration, and a programming-free GUI. SHARCQ is a great way to improve cell quantification, registration, and visualization in a user friendly way.

This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications. SHARCQ Software: RRID: SCR_022498

Read the Paper!

             Read more about the project in the eNeuro paper!

GitHub Repository

Get access to necessary files and code on their GitHub repository!

Have questions? Send us an email!