Ultrasound matrix imaging for 3D transcranial in-vivo localization microscopy

Ultrasound data associated to the paper "Ultrasound matrix imaging for 3D transcranial in-vivo localization microscopy".

Abstract : "Transcranial ultrasound imaging is usually limited by skull-induced attenuation and high-order aberrations. By using contrast agents such as microbubbles in combination with ultrafast imaging, not only can the signal-to-noise ratio be improved, but super-resolution images down to the micrometer scale of the brain vessels can be obtained. However, ultrasound localization microscopy (ULM) remains impacted by wave-front distortions that limit the microbubble detection rate and hamper their localization. In this work, we show how ultrasound matrix imaging (UMI), which relies on the prior recording of the reflection matrix, can provide a solution to those fundamental issues. As an experimental proof-of-concept, an in-vivo reconstruction of deep brain microvessels is performed on three anesthetized sheeps. The compensation of wave distortions is shown to drastically enhance the contrast and resolution of ULM. This experimental study thus opens up promising perspectives for a transcranial and non-ionizing observation of human cerebral microvascular pathologies, such as stroke."

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Data ("UMI_data.zip") and code ("UMI_code.zip") associated to UMI:

• Raw data (recorded reflection matrix) associated to the three different sheep (n°4, 5 and 6):
  • "Sheep_4_0428_112712_UMI_raw.mat"
  • "Sheep_5_0531_112114_UMI_raw.mat"
  • "Sheep_5_0601_114350_UMI_raw.mat"
  • "Sheep_6_0617_103257_UMI_raw.mat"
  • "Sheep_6_0617_133256_UMI_raw.mat"
  • "Sheep_6_0707_114840_UMI_raw.mat"
  • "Sheep_6_0708_123612_UMI_raw.mat"
• Partially processed data - Focused reflection matrix (after beamforming) for a single acquisition of the sheep n°6 at depths [55-57.5] mm:
  • "Sheep_6_0707_114840_Z_55__57.5_UMI_focused_reflection_matrix.mat"
• Code associated to UMI ("UMI_code.zip") :
  • Aberration law extraction (panel C of Figure n°4)
  • RPSF map extraction (panel B and D of Figure n°4)
  • The main script is "UMI_post_processing.m", other files are sub-functions.

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Data and code associated to ULM:

• ULM tracks (ULM_tracks.zip). For each dataset, the number at the end of the ‘.mat’ file refers to a given frame of the ultra-fast movie recorded for ULM processing. 
• Final ULM volume (ULM_volume.zip) without ("original") and with UMI correction ("corrected"):
  • "Sheep_4_0428_103503" 
    
    • "Sheep_4_0428_103503_ULM_original.mat"
    • "Sheep_4_0428_103503_ULM_corrected.mat" (associated correction sequence : "Sheep_4_0428_112712_UMI_raw.mat")
  • "Sheep_5_0531_110031"
    • "Sheep_5_0531_110031_ULM_original.mat"
    • "Sheep_5_0531_110031_ULM_corrected.mat" (associated correction sequence : "Sheep_5_0531_112114_UMI_raw.mat")
  • "Sheep_5_0601_110407"
    • "Sheep_5_0601_110407_ULM_original.mat"
    • "Sheep_5_0601_110407_ULM_corrected.mat" (associated correction sequence : "Sheep_5_0601_114350_UMI_raw.mat")
  • "Sheep_6_0617_104051"
    • "Sheep_6_0617_104051_ULM_original.mat"
    • "Sheep_6_0617_104051_ULM_corrected.mat" (associated correction sequence : "Sheep_6_0617_103257_UMI_raw.mat")
  • "Sheep_6_0617_105802"
    • "Sheep_6_0617_105802_ULM_original.mat"
    • "Sheep_6_0617_105802_ULM_corrected.mat" (associated correction sequence : "Sheep_6_0617_103257_UMI_raw.mat")
  • "Sheep_6_0617_131123"
    • "Sheep_6_0617_131123_ULM_original.mat"
    • "Sheep_6_0617_131123_ULM_corrected.mat" (associated correction sequence : "Sheep_6_0617_133256_UMI_raw.mat")
  • "Sheep_6_0707_130007"
    • "Sheep_6_0707_130007_ULM_original.mat"
    • "Sheep_6_0707_130007_ULM_corrected.mat" (associated correction sequence : "Sheep_6_0707_114840_UMI_raw.mat")
  • "Sheep_6_0708_133317"
    • "Sheep_6_0708_133317_ULM_original.mat"
    • "Sheep_6_0708_133317_ULM_corrected.mat" (associated correction sequence : "Sheep_6_0708_123612_UMI_raw.mat")
  • Code "Display_3D.m" allows visualizing a 3D ULM volume as a MIP (Maximum Intensity Projection) on Matlab.