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Merge pull request #901 from zacsimile/ff-fix
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docs/source/user_guide/file_formats.rst

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@@ -10,8 +10,8 @@ as Zarr, N5, and HDF5, including OME-Zarr, cater to the needs of large-scale,
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multi-dimensional datasets by enabling efficient data storage, access, and processing at
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cloud-compute scales.
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To enable ambitious imaging projects, **navigate** **navigate** comes pre-packaged with TIFF, OME-TIFF, OME-Zarr, HDF5/N5
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(`BigDataViewer <https://imagej.net/plugins/bdv/>`_) file saving formats.
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To enable ambitious imaging projects, **navigate** comes pre-packaged with TIFF, OME-TIFF, OME-Zarr,
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and HDF5/N5 (`BigDataViewer <https://imagej.net/plugins/bdv/>`_) file saving formats.
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OME, or Open Microscopy Environment, is a standardized metadata model that ensures
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that imaging data can be accurately understood, shared, and analyzed across different software
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platforms and research groups.
@@ -63,7 +63,7 @@ OME-TIFF, H5, N5, and OME-Zarr formats across image resolutions of 512x512,
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1024x1024, and 2048x2048 under two conditions: (A) capturing 1000 single-plane
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images and (B) acquiring a single z-stack composed of 1000 planes. All times
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are measured in milliseconds. Results are presented below. For z-stack imaging, TIFF
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and OME-TIFF formats achieved write speeds of up to approximately 400 Hz for a 2048x2048 camera
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and OME-TIFF formats achieved write speeds of up to approximately 300 Hz for a 2048x2048 camera
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resolution, surpassing the operational speeds of most contemporary sCMOS cameras.
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The Big-TIFF variant was used for both TIFF and OME-TIFF formats to accommodate the
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large file sizes.
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+-------------+---------+----------+-------+-------+---------+
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| | TIFF | OME-TIFF | H5 | N5 | OME-Zarr|
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+=============+=========+==========+=======+=======+=========+
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| 512x512 | 0.83 | 10.0 | 1.69 | 3.02 | 1.09 |
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| 512x512 | 1.19 | 29.24 | 3.17 | 9.00 | 5.30 |
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+-------------+---------+----------+-------+-------+---------+
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| 1024x1024 | 1.55 | 10.4 | 6.46 | 5.70 | 2.27 |
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| 1024x1024 | 1.84 | 36.69 | 18.59 | 14.55 | 8.81 |
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+-------------+---------+----------+-------+-------+---------+
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| 2048x2048 | 11.2 | 38.6 | 28.8 | 19.6 | 11.6 |
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| 2048x2048 | 5.55 | 44.65 | 84.18 | 38.60 | 25.02 |
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+-------------+---------+----------+-------+-------+---------+
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Z-Stack Imaging
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+--------------+---------+----------+-------+-------+---------+
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| | TIFF | OME-TIFF | H5 | N5 | OME-Zarr|
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+==============+=========+==========+=======+=======+=========+
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| 512x512 | 0.14 | 0.13 | 2.64 | 1.58 | 1.05 |
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| 512x512 | 0.28 | 0.25 | 7.30 | 5.10 | 3.29 |
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+--------------+---------+----------+-------+-------+---------+
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| 1024x1024 | 0.49 | 0.48 | 10.6 | 5.08 | 4.06 |
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| 1024x1024 | 0.89 | 0.88 | 29.15 | 12.44 | 8.26 |
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+--------------+---------+----------+-------+-------+---------+
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| 2048x2048 | 1.92 | 1.86 | 52.7 | 13.90 | 8.50 |
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| 2048x2048 | 4.12 | 3.30 | 135.74| 37.09 | 24.83 |
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+--------------+---------+----------+-------+-------+---------+
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Additional Sources of Overhead
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Computer Specifications for Benchmarks
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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The computer specifications that the benchmarks were performed on are as follows:
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The computer specifications that the benchmarks were performed on are as follows.
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- Architecture: x86_64
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- CPU operational modes: 32-bit, 64-bit
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- Number of CPUs: 72
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- Threads per core: 2
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- Cores per socket: 18
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- CPU Model: Intel(R) Xeon(R) Gold 6354 CPU @ 3.00GHz
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- CPU Speed: 883.850 MHz
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- Memory: 0.5 TB
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- CPU: Intel(R) Xeon(R) Silver 4112 CPU @ 2.60GHz
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- Memory: 88 GB
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- Hard Drive: Micron 5200 ECO 7680gb SSD

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