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FEMTOSmart Software

FEMTOSmart software packs a range of features indispensable for efficient data acquisition, visualization and analysis. The clean, ergonomic user interface has been condensed from the experience of many scientists who have been using the FEMTOSmart microscopy platform.

Key features:

  • integrated control of all hardware units: focusing, resonant and galvo scanners, PMTs, Pockels cells, light path actuators, auxiliary digital and analog channels, XY(Z) stages,
  • live preview mode with on-the-fly adjustment of acquisition parameters,
  • live display and processing during data acquisition,
  • fast Z-stack recording,
  • volumetric imaging,
  • 2D Multi-ROI scanning and photostimulation methods,
  • dual scanning option: resonant scanner based fast imaging with simultaneous galvanometric scanner based photostimulation,
  • special scanning methods for microscopes having a non-resonant galvo scanner are available in the MES 6.5 software package that can work in tandem with FEMTOSmart software.

Flexible and efficient data management

Resonant scanners acquire multichannel full field of view images at 30 frames per second (fps) and can even reach 1000 fps while recording from a smaller region. FEMTOSmart software handles the high data rates produced during acquisition with an optimized data handling architecture that can stream data to disk in real-time. Therefore, only storage size will limit the length of the experiment. The optimized data pipeline of the FEMTOSmart software features:

  • digital lab-book format: different types of measurements and user-defined metadata can be grouped into sessions and saved into one file,
  • optimized, unlimited data streaming to disk into open-standard HDF5 format,
  • state-of-the-art lossless compression algorithm to reduce data size,
  • data exporting into standard microscopy file formats,
  • convenient and fast data browser for measurement visualization and processing,
  • pervasive auto-save and data rescue.

Simultaneous activity imaging and photostimulation

The FEMTOSmart software supports truly simultaneous multichannel imaging and photostimulation on hardware configurations equipped with two light paths (FEMTOSmart Dual). Cellular and subcellular structures can be photostimulated at user-positioned points, line segments or spirals. Light can be precisely dosed via the experiment protocol editor in which the user can quickly set up waveforms with millisecond precision to control light-path elements.

Region of interest visualization and analysis

Regions of interest (ROIs) can be selected in order to perform select real-time calculations simultaneously with image acquisition. ROIs may be chosen in various shapes and, for photoactivation, can be grouped together as separate populations. Possible ROI calculations include:

  • intensity as a function of time,
  • mean, minimum, and maximum intensity,
  • standard deviation,
  • dF/F,
  • ratiometric imaging.

Application Programming Interface (FemtoAPI)

The application programming interface for our FEMTOSmart microscopy platform (FemtoAPI) lets you control your Femtonics microscope with MATLAB and Python scripts. Via FemtoAPI, one can create custom measurement protocols and integrate Femtonics microscopes to other lab software environments.

FemtoAPI based extensions of FEMTOSmart microscopes allow

  • time-lapse 3D imaging,
  • extension of the field of view via tiled imaging,
  • triggering measurements with external devices,
  • integrating community based open-source data visualization and analysis tools.

If you are interested in FemtoAPI, contact us!


The FEMTOSmart software (MESC 4.0) for FEMTOSmart 2D systems.


Minimum system requirements

  • Any computer running Microsoft® Windows® 10
  • RAM: At least 16 GB
  • Disk space: At least 100 GB free disk space
  • Display: At least 1280×720 pixels resolution
  • MATLAB r2018a-r2020a