Femtonics - FEMTO3D Atlas Software - Femtonics

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 features of conventional multiphoton systems including:

  • 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.

3D acquisition features that make Atlas a versatile, ultra-fast multiphoton experimental platform:

  • volumetric imaging,
  • a variety of 3D region scanning methods,
  • computer-assisted cell extraction from volumetric data,
  • 3D photostimulation with imaging,
  • anti-motion technology for acquiring stable data from behaving animals,
  • high-speed frame scanning along any plane orientation in 3D.

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

  • 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 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).

Community-validated open software interface

Users new to multiphoton imaging or those who have already worked with conventional microscopes can get quickly started with the entry-level software interface. Experienced users can customize the full-feature interface to maximize their efficiency of data collection. For those pioneering new experimental workflows, our developer team can provide customized solutions in a collaborative setting. We continue to develop Atlas software to provide the scientific community with the most versatile and efficient image acquisition and analysis environment. Users new to multiphoton imaging or those who have already worked with conventional microscopes can get quickly started with the entry-level software interface. Experienced users can customize the full-feature interface to maximize their efficiency of data collection. For those pioneering new experimental workflows, our developer team can provide customized solutions in a collaborative setting.

3D region scanning methods

Atlas software supports setting up experiments that make the most of available 3D region scanning modes. Supported 3D region scanning methods are

  • 3D random-access point scanning,
  • multiple line scanning/3D trajectory scanning,
  • multiple area scanning: chessboard and ribbon scanning,
  • scanning various volume elements: multi-cube and snake scanning,
  • high-speed arbitrary frame scanning,
  • volume scanning.

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.

Download

The FEMTO3D Atlas software (MES 7.4) for FEMTO3D systems. Files containing high-speed arbitrary frame scanning data can be opened via an optional module.

 
 
 
 
 

Minimum system requirements

  • Windows 10
  • MATLAB R2018a 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