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FLOW CYTOMETRY DATA COMPRESSION A.E. Bras PhD Student Erasmus - PowerPoint PPT Presentation

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FLOW CYTOMETRY DATA COMPRESSION A.E. Bras PhD Student Erasmus University, Rotterdam, the Netherlands Flow Cytometry Flow Cytometry Flow Cytometry Flow Cytometry Flow Cytometry Flow Cytometry Older Systems Older Systems Newer Systems

  1. FLOW CYTOMETRY – DATA COMPRESSION A.E. Bras PhD Student Erasmus University, Rotterdam, the Netherlands

  2. Flow Cytometry

  3. Flow Cytometry

  4. Flow Cytometry

  5. Flow Cytometry

  6. Flow Cytometry

  7. Flow Cytometry

  8. Older Systems

  9. Older Systems

  10. Newer Systems

  11. Newer Systems

  12. Newer Systems

  13. Newer Systems FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  14. Newer Systems FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  15. Storage FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  16. Storage .FCS FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  17. Storage FLOW CYTOMETRY STRANDARD .FCS FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  18. Storage FLOW CYTOMETRY STRANDARD .FCS PRO WIDELEY USED FLOATING POINT DATA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  19. Storage FLOW CYTOMETRY STRANDARD .FCS PRO WIDELEY USED FLOATING POINT DATA - - - - - - - - - - - - CON - - - - - - - - - - - - NO COMPRESSION - - - - - - - - - - - - MILLIONS - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

  20. Lossless Compression .FCS

  21. Lossless Compression .FCS ≈ 70 % .ZIP

  22. Lossless Compression .FCS ≈ 70 % .ZIP Better alternative?

  23. Lossless Compression - Benchmark

  24. Lossless Compression - Benchmark .FCS 167.131

  25. Lossless Compression - Benchmark RANDOM .FCS 167.131

  26. Lossless Compression - Benchmark RANDOM .FCS 167.131

  27. Lossless Compression - Benchmark CODEC RATIO CODEC RATIO LZIP 0.533 ZPAQ 0.460 LZMA 0.533 BCM 0.510 XZ 0.533 LZIP 0.533 GLZA 0.558 LZMA 0.533 LZHAM 0.568 FLZMA2 0.539 CSC 0.590 LZHAM 0.569 BROTLI 0.598 BROTLI 0.571 TORNADO 0.622 BZIP2 0.580 ZSTD 0.626 CSC 0.590 XPACK 0.637 BALZ 0.598 ZLING 0.665 XPACK 0.612 LIBDEFLATE 0.676 ZSTD 0.625 LZFSE 0.690 ZOPFLI 0.674 RANDOM CRUSH 0.692 LIBDEFLATE 0.676 ZLIB 0.695 LZFSE 0.690 UCL_NRV2D 0.725 CRUSH 0.692 UCL_NRV2E 0.725 ZLIB 0.695 UCL_NRV2B 0.734 BRIEFLZ 0.727 LZO1X 0.755 DOBOZ 0.750 LZO1Z 0.757 LZSSE8 0.758 LZSSE8 0.758 BSCQLFC 0.763 LZO1Y 0.768 LZSSE2 0.768 LZSSE2 0.768 LZ4 0.777 LIZARD 0.770 LZSSE4 0.781 DENSITY 0.771 LZG 0.803 .FCS LZO2A 0.774 SUBOTIN 0.819 LZO1B 0.775 FASTAC 0.819 LZ4HC 0.777 ZLIBH 0.823 167.131 ... ... ... ...

  28. Lossless Compression - Benchmark CODEC RATIO CODEC RATIO LZIP 0.533 ZPAQ 0.460 LZMA 0.533 BCM 0.510 XZ 0.533 LZIP 0.533 GLZA 0.558 LZMA 0.533 LZHAM 0.568 FLZMA2 0.539 CSC 0.590 LZHAM 0.569 BROTLI 0.598 BROTLI 0.571 TORNADO 0.622 BZIP2 0.580 ZSTD 0.626 CSC 0.590 XPACK 0.637 BALZ 0.598 ZLING 0.665 XPACK 0.612 LIBDEFLATE 0.676 ZSTD 0.625 LZFSE 0.690 ZOPFLI 0.674 RANDOM CRUSH 0.692 LIBDEFLATE 0.676 ZLIB 0.695 LZFSE 0.690 UCL_NRV2D 0.725 CRUSH 0.692 UCL_NRV2E 0.725 ZLIB 0.695 UCL_NRV2B 0.734 BRIEFLZ 0.727 LZO1X 0.755 DOBOZ 0.750 LZO1Z 0.757 LZSSE8 0.758 LZSSE8 0.758 BSCQLFC 0.763 LZO1Y 0.768 LZSSE2 0.768 LZSSE2 0.768 LZ4 0.777 LIZARD 0.770 LZSSE4 0.781 DENSITY 0.771 LZG 0.803 .FCS LZO2A 0.774 SUBOTIN 0.819 LZO1B 0.775 FASTAC 0.819 LZ4HC 0.777 ZLIBH 0.823 167.131 ... ... ... ...

  29. Lossless Compression - Benchmark CODEC RATIO CODEC RATIO LZIP 0.533 ZPAQ 0.460 LZMA 0.533 BCM 0.510 XZ 0.533 LZIP 0.533 GLZA 0.558 LZMA 0.533 LZHAM 0.568 FLZMA2 0.539 CSC 0.590 LZHAM 0.569 BROTLI 0.598 BROTLI 0.571 TORNADO 0.622 BZIP2 0.580 ZSTD 0.626 CSC 0.590 XPACK 0.637 BALZ 0.598 ZLING 0.665 XPACK 0.612 LIBDEFLATE 0.676 ZSTD 0.625 LZFSE 0.690 ZOPFLI 0.674 CRUSH 0.692 LIBDEFLATE 0.676 ZLIB 0.695 LZFSE 0.690 UCL_NRV2D 0.725 CRUSH 0.692 UCL_NRV2E 0.725 ZLIB 0.695 UCL_NRV2B 0.734 BRIEFLZ 0.727 LZO1X 0.755 DOBOZ 0.750 LZO1Z 0.757 LZSSE8 0.758 LZSSE8 0.758 BSCQLFC 0.763 LZO1Y 0.768 LZSSE2 0.768 LZSSE2 0.768 LZ4 0.777 LIZARD 0.770 LZSSE4 0.781 DENSITY 0.771 LZG 0.803 .FCS LZO2A 0.774 SUBOTIN 0.819 LZO1B 0.775 FASTAC 0.819 LZ4HC 0.777 ZLIBH 0.823 167.131 ... ... ... ...

  30. Lossless Compression - Benchmark

  31. Lossless Compression - Benchmark ≈ 0.45

  32. Implementation in R

  33. Implementation in R base::memCompress(type=" XZ ")

  34. Implementation in R base::memCompress(type=" XZ ")

  35. Bioconductor - flowCore

  36. Bioconductor - flowCore

  37. Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS C:\output.fcs

  38. Bioconductor - flowCore base::readBin C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS C:\output.fcs

  39. Bioconductor - flowCore base::readBin C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS base::writeBin C:\output.fcs

  40. Bioconductor - flowCore base::readBin C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS base::memCompress base::writeBin C:\output.fcs

  41. Bioconductor - flowCore base::readBin C:\input.fcs base::memDecompress flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS base::memCompress base::writeBin C:\output.fcs

  42. Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .TAR.GZ C:\output.fcs

  43. Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .TAR.GZ C:\output.fcs

  44. Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .TAR.GZ C:\output.fcs

  45. Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .FCS.XZ C:\output.fcs

  46. Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .FCS.XZ C:\output.fcs

  47. Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .FCS.XZ C:\output.fcs

  48. Bioconductor - flowCore C:\input.fcs flowCore::read.FCS flowSom::FlowSOM flowCore::write.FCS .FCS.XZ C:\output.fcs

  49. Bioconductor – flowCore - Pipelines

  50. Bioconductor – flowCore - Pipeline C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet flowCore::write.flowSet C:\output\01.fcs C:\output\02.fcs

  51. Bioconductor – flowCore - Pipeline C:\input.zip base::unzip C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet flowCore::write.flowSet C:\output\01.fcs C:\output\02.fcs

  52. Bioconductor – flowCore - Pipeline C:\input.zip base::unzip C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet flowCore::write.flowSet C:\output\01.fcs C:\output\02.fcs base::zip C:\output.zip

  53. Bioconductor – flowCore - Pipeline C:\input.zip base::unzip C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet flowCore::write.flowSet C:\output\01.fcs C:\output\02.fcs base::zip C:\output.zip

  54. Bioconductor – flowCore - Pipeline C:\input.zip base::unzip C:\input\01.fcs C:\input\02.fcs flowCore::read.flowSet ARCHIVAL flowCore::write.flowSet CYTOMETRY STANDARD C:\output\01.fcs C:\output\02.fcs .ACS base::zip C:\output.zip

  55. Bioconductor – flowCore - Pipeline = ARCHIVAL CYTOMETRY STANDARD .ACS .ZIP

  56. Bioconductor – flowCore - Pipeline = ARCHIVAL CYTOMETRY .FCS .FCS .FCS STANDARD .ACS .ZIP

  57. Bioconductor – flowCore - Pipeline .TXT = ARCHIVAL CYTOMETRY .FCS .FCS .FCS STANDARD .ACS .ZIP

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