HistoMatch - Atlas/Histology Matching

HistoMatch is a powerful, easy-to-use software tool for interactive atlas/histology matching. It supports straightforward digitization of histological preparations, rapid identification, assignment and fitting of the best histological slice containing the brain region of interest to the correspondent atlas slice.

  • Histology Slice Digitization
  • Smart Atlas Matching
  • Intuitive Slice Manipulation
  • Rat & Mouse Brain Slices
  • High Throughput Analysis
  • Easy-To-Use

You can use this powerful tool to further correct atlas-localization discrepancies by histological feedback, and to significantly enhance the insight on the electrophysiological mapping.

HistoMatch offers a user-friendly importing-matching-embedding scenario in a comfortable wizard mode:

  • start with a histology glass slide with a matrix of slices
  • scan and save a digital image of the whole slide
  • import the image in HistoMatch
  • HistoMatch automatically detects and extracts the slices, creating a scrollable slideshow
  • then, the program identifies and assigns the histological slices that best fit the given atlas sections for the brain region of interest
  • the next wizard step offers the versatile tools necessary for the fine adjustment/tuning between the atlas section and the corresponding histological slice (translation, rotation, anchored stretching and scaling)
  • the identification and alignment procedures support the utilization of relevant landmarks, exploration traces and localization markers (e.g., iontophoretic or electrolytic depositions)
  • the results of the matching procedure are exported to the main Reco application, enabling optimal correction of the trajectory-atlas spatial correlation


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