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FEMTO3D Atlas Software

FEMTO3D Atlas is a unique hardware platform that offers the greatest flexibility for your experiments. The power and flexibility of FEMTO3D Atlas hardware can be harnessed through Atlas Software that has been developed for and validated by numerous experimentalists from many labs.

Key features

Atlas incorporates all features of conventional multiphoton systems while 3D acquisition features make Atlas a versatile, ultra-fast multiphoton experimental platform including:

  • 3D real-time motion correction for all scanning modes (FocusPinner: FPGA-based, correction loop time < 1 ms) 
  • a variety of 3D region scanning methods
    • 3D random-access point scanning 
    • multiple line scanning/3D trajectory scanning 
    • multiple area scanning: chessboard and ribbon scanning 
    • multiple volume scanning: multicube and snake scanning
  • advanced 3D photostimulation with imaging 
  • volumetric imaging 
  • fast point scanning with sampling rate of 100 kHz 
  • integrated control of all hardware units: acousto-optic scanner, PMTs, beam-stabilizer, light path actuators, auxiliary digital and analog channels, XY(Z) stages 
  • epi illumination and camera handling 
  • live preview mode with on-the-fly measurement parameter adjustment 
  • live display and processing during data acquisition 
  • fast Z-stack recording 
  • computer-assisted cell extraction from volumetric data 
  • post-hoc motion correction 
  • high-speed frame scanning along any plane orientation in 3D 
  • image overlay for chronic imaging 

Flexible and efficient data management

Modern high-speed microscopy experiments require a data processing pipeline that allows quick and on-line visualizations and analysis. We have been spending our development efforts on making Atlas Software among the best in the field by offering users with 

  • integrated rendering of 3D volumes and object recognition with Imaris
  • digital lab-book storage format: entire measurement series with different types of measurements can be saved into one file, including per-measurement metadata, 
  • optimized, unlimited data streaming to disk into open-standard HDF5 format in high-speed frame acquisition mode,
  • data can be accessed during measurement as well with FemtoAPI
  • data exporting into standard microscopy file formats,
  • convenient and fast data browser for measurement visualization and processing,
  • pervasive auto-save and data rescue,
  • automation and batch data analysis via application programming interface (API).

Simultaneous activity imaging and photostimulation

All scanning modes implemented in Atlas can be combined with photostimulation. Users can simply use the 3D visualization and annotation toolset implemented in Atlas software to configure which regions to target with photostimulation. 

A microscope software to advance your research

Discover how can you benefit from the custom software solutions tailored to your specific needs.


The FEMTO3D Atlas software (MES 8.3) for FEMTO3D systems. Files containing high-speed arbitrary frame scanning data can be opened via an optional module.

To request an analysis version of MES, please download and run the LicenceRequest.exe application that will monitor the technical information required to run the MES software on your PC.



Main new features in MES 8.3 

  • Real-time motion correction for all scanning modes (including ZStacks)
  • Increased number of predefined patterns (over 80)
  • Break view at Live imaging for special scanning measurements
  • Special scan browser show the pixel timestamp (total time counted from the beginning of the measurement) 
  • Improved 3D real-time motion correction, FocusPinner 
  • Automatic adjustment of ROIs after reselecting the reference point 
  • Combination with dichro functionality 
  • Frame Sync signal adjustment 
  • Image overlay functionality for chronic imaging 
  • 100 kHz sampling rate per points  
  • Common template at post-hoc motion correction for several special scanning modes 
  • Camera and 2p images are matched with haircross 
  • Automatized adjusting of ROIs after reselecting reference point 
  • Shorter precalculation time 
  • Support for Basler acA5472-17um camera (5472 px x 3648 px, with a sensor size of 13.1 mm x 8.8 mm) 
  • Supporting Suite2p and FIOLA packages for cell and Ca2+ signal extraction 
  • Win11 compatibility

Minimum system requirements

  • Windows 10
  • MATLAB 2020b or a newer version
  • Image Processing Toolbox
  • Signal Processing Toolbox
  • RAM: At least 16 GB
  • Disk space: At least 100 GB free disk space
  • Display: At least 1280×720 pixels resolution