Skip to content


Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?

Latest commit


Git stats


Failed to load latest commit information.
Latest commit message
Commit time

CHEndoscope Overview

Complete instructions on how to use the CHEndoscope, including assembly, surgery, behavioural protocols and data analysis can be in the CHEndoscope protocols paper.

  1. Assembling your CHEndoscope

  2. Acquiring images with your CHEndoscope

  3. Analysis of calcium imaging videos uses CHEndoscope-minipipe

Assembling your CHEndoscope

The CHEndoscope consists of 4 plastic components that can be 3D printed

3D printed components of the CHEndoscope

When printing these parts, we recommend a print resolution of at most 100μm (50μm works best in our hands). Our lab has experimented with various FDM, SLA and material jetting printers, and find that SLA printers such as the Formlabs Form2 render best results. FDM printers often lack the resolution required to render the fine threads and internal details of several CHEndoscope parts. In addition to print resolution, make sure the material you are printing with does not fluoresce or otherwise interfere with the imaging path when exposed to 470nm or 535nm light.

Download CHEndoscope STL files for 3D printing, or STEP files if you want to modify the base CHEndoscope design.

Acquiring images with your CHEndoscope

In order to capture images from the CHEndoscope, you will need to install acquisition software that interfaces with the CHEndoscope's Ximea USB camera. This code is compatible with Linux and Windows systems.


For Windows

Running the acquisition software

  1. Open a new cmd window

    • cd [path for storing video files]
    • python "path\to\"
  2. To change gains/exposure etc:

    • Open a second cmd window and run ncat -u 6557
    • Then type for example: [set_gain 10]


Compact Head-mounted Endoscope for calcium imaging in mice.






No releases published


No packages published