The control features of software driving Femtonics microscopes has improved with advanced driving algorithms for the acousto-optic scanner to deliver imaging data comparable to electrophysiological recordings. The high-mathematical theories translated to high-level programming led to those developments that enable you to measure only the interesting parts and skip the other parts of the 3D sample with astonishing measurement speed tracking the physiological events or to high level of motion correction during imaging somata, dendrites and spines.

Control and integration

The control software is capable of performing all standard microscopy functions and it fully integrates the control of all hardware units in the microscope: camera handling, focusing, laser intensity, light path actuators, electrical devices, scanner, PMT sensitivity, auxiliary digital and analog channels to interface stimulators, behavior control devices, sample stage and pipette manipulator devices. Measurement automatization helps the researchers on the timescale of seconds by letting them run freely composed sequences of image acquisition and other measurement protocols.

Analysis functions

Our measurement control software offers a wide range of specialized analysis tools. Beside to the numerous scanning patterns and 3D ROI selection, it allows quantitative intensity-based calculations for following real-time fluorescence changes, simultaneous analysis for single measurements and batch analysis, or simultaneous recording and alignment of fluorescent and electrophysiological data. Our developer team is collaborating with researchers from various fields to provide you with a software that makes experimental work efficient.


3D localization of cells in Z-stacks

This module finds cell centers in 3D image stacks as a set of points. The generated point sets can be used for measurements or for the photo stimulation of cells in a random-access fashion. Recommended for the fast selection of a large number of ROIs for network imaging.

Ratio Imaging

Implements two-channel ratio imaging analysis calculations

This module offers different types of dG/R and G/R calculations in the measurement viewer windows and batch analysis tools:

  • real-time ratio metric analysis of two channel measurements (dG/R),
  • possibility to calculate dG/R images of the raw line-scan data,
  • adds dG/R analysis tools for batch analysis panels,
  • selectable source channels,
  • automatic background calculation algorithms for both channels,
  • running averaging before or after division.


Running custom user scripts during measurements

It enables you to define custom MATLAB functions to be called before or after a measurement is performed. Useful for pre-measurement signaling or post-measurement modification of data, annotation, or analysis. DoCallBack includes sample code for e.g. waiting for a trigger, parallel camera acquisition, and automatic TIFF export. Recommended for behavioral studies.

Visual stimulation player

Integrated visual stimulus player

This module allows loading and sequentially playing videos or images for visual stimulus and other stimuli can be triggered such as tactile, whisker, auditory or odor stimuli. The stimuli can be triggered by software or TTL signals. Recommended for behavioral studies.

Electrophysiology software module

Simple electrophysiology functions commanded from MES

This module acquires electrophysiology signals using the A/D converters of the microscope. The telegraphing function communicates the conversion parameters from the amplifier to the A/D converters controlled by MES. Convenient acquisition of electrophysiology signals time is aligned with the imaging data. The electrophysiology GUI includes a seal test window, too. Supported amplifiers: MultiClamp700B

Electrophysiology data importer

Importing electrophysiology data

With this module, user can import externally recorded electrophysiology curves into MES measurement units. Imaging with MES works simultaneously with the external digitizer by triggering each sweep of electrophysiology recording. An easy-to-use tool helps matching sweeps in the electrophysiology files and MES measurement units and also imports electrophysiology curves to the optical data. Hundreds of curves can be loaded at the end of the measurement with a few clicks. The module allows importing electrophysiology data directly into the Curve analysis window of MES.

Correct motions

Anti-motion technology is based on a mathematical theory which has been translated into the highest level of computational programming and implemented in the microscope control software. It has been developed for correcting motions caused by vessel pulsing, respiration, locomotion, or behavior and preserving the fluorescent data.