Software

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 FEMTO3D Atlas Software that has been developed for and validated by numerous experimentalists from many labs.

Key features

FEMTO3D Atlas incorporates all features of conventional multiphoton systems while 3D acquisition features make FEMTO3D Atlas a versatile, ultra-fast multiphoton experimental platform including.

• 3D Real-Time Motion Correction for all Scanning Modes
  (3D-RTMC: FPGA-based, correction loop time < 1 ms)
• 3D Region Scanning Methods:
  • 3D Random-Access Point Scanning
  • Multiple line scanning: 3D Multi-Line/3D Trajectory-Line Scanning
  • Multiple area scanning: 3D Chessboard and 3D Ribbon Scanning
  • Multiple volume scanning: 3D Multi-cube and 3D 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 Arbitrary 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 FEMTO3D Atlas software to configure which regions to target with photostimulation.

Main new features in MES 8.5

• TileScan and TileZScan measurement modules
  • Tilings can be called from MetaProtocol
  • Images are stitched in Fiji and a separate measurement unit is created
• Measurement control panels can be opened in separate windows
• 3D-RTMC improvements
  • Correction can be turned on/off during measurements
  • Reference point can be changed during measurements
  • Option to turn off correction in the Z direction
  • Shows stability diagram after selecting the reference area
  • It works during Raster scan Capture as well
• New option for Advanced Intensity Compensation:
  • save compensated amplitudes and RAM factors as separate measurement units in the background session
  • Recorded analog/digital input data is continuously streamed to the disk instead of storing in RAM until the end of the measurement. This solves the slowing of MES after long measurements

Minimum system requirements