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Merge remote-tracking branch 'upstream/develop' into fix-loading-plugin-error
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‎docs/source/contributing/software_architecture.rst‎

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@@ -6,6 +6,8 @@ Software Architecture
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:align: center
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:alt: Software Architecture
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------------------
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.. _software-architecture-section:
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Model View Controller (MVC)
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It relays user input in the form of traces and commands to the model and relays model
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output in the form of images and data to the view.
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------------------
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Communication Enhancements
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----------------------------
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Extendability
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============================
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To maximize the extendability of **navigate**, it incorporates:
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- **Plugin Layer**: Offers the flexibility to integrate non-supported devices through
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plugins, enhancing the system's adaptability to various hardware.
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------------------
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Data Acquisition and Processing
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--------------------------------
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===============================
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**navigate** employs a feature container for running acquisition routines, characterized by:
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**navigate** during run-time. Image analysis is performed on images in memory that are
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stored as numpy arrays, ensuring rapid processing.
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------------------
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Feature Lists
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-------------------
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============================
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Feature lists are highly versatile, capable of:
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‎docs/source/index.rst‎

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:caption: User Guide
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:maxdepth: 1
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user_guide/hardware_overview
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user_guide/hardware/hardware_home
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user_guide/file_formats
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user_guide/gui_walkthrough
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user_guide/setup_microscope

‎docs/source/user_guide/file_formats.rst‎

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@@ -3,10 +3,10 @@ Supported File Formats
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======================
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The choice of file format for saving imaging data in microscopy is crucial
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because it affects data integrity, accessibility, and analysis efficiency.
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because it affects write speed, data integrity, accessibility, and analysis efficiency.
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Formats like TIFF and its derivative OME-TIFF are widely used due to their ability
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to store metadata and support multiple imaging channels. However, modern formats such
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as Zarr, N5, and HDF5, including OME-ZARR, cater to the needs of large-scale,
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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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----------------
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BigDataViewer H5/N5/OME-Zarr
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BigDataViewer H5/N5
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----------------------------
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**navigate** uses `h5py <https://docs.h5py.org/en/stable/index.html>`_ (H5) and
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`zarr <https://zarr.readthedocs.io/en/stable/>`_ (N5) to store data in a BigDataViewer
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file format. This is a pyramidal format, necessitating the saving of both the original
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data and down sampled versions of this data. The additional data slows down the write
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speed. The N5 format is faster than H5 because it allows multithreaded writes.
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speed. The N5 format can be faster than H5 because it allows for multithreaded writes.
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OME-Zarr
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--------
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OME-Zarr is a Zarr file format that adheres to strict metadata specifications, detailed
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at https://ngff.openmicroscopy.org/0.4/index.html. It allows for pyramidal data writing,
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storage of segmentation labels with the data set, and updating the pyramidal structure
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on the fly.
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----------------
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Image Writing Benchmarks
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------------------------
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To evaluate the performance of saving imaging data in different formats, we conducted
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benchmarks on a Linux-based system. We assessed the median disk write time for TIFF,
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benchmarks on a RedHat Linux system. We assessed the median disk write time for TIFF,
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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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+-------------+---------+----------+-------+-------+---------+
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| | TIFF | OME-TIFF | H5 | N5 | OME-Zarr|
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+=============+=========+==========+=======+=======+=========+
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| 512x512 | 4.06 | 15.26 | 2.79 | 12.09 | 1.35 |
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| 512x512 | 0.83 | 10.0 | 1.69 | 3.02 | 1.09 |
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+-------------+---------+----------+-------+-------+---------+
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| 1024x1024 | 6.69 | 15.25 | 8.33 | 14.74 | 2.46 |
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| 1024x1024 | 1.55 | 10.4 | 6.46 | 5.70 | 2.27 |
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+-------------+---------+----------+-------+-------+---------+
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| 2048x2048 | 22.25 | 38.57 | 34.71 | 29.56 | 11.85 |
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| 2048x2048 | 11.2 | 38.6 | 28.8 | 19.6 | 11.6 |
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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 | 0.21 | 0.17 | 4.76 | 1.80 | 1.30 |
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| 512x512 | 0.14 | 0.13 | 2.64 | 1.58 | 1.05 |
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+--------------+---------+----------+-------+-------+---------+
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| 1024x1024 | 0.52 | 0.57 | 15.70 | 5.38 | 4.22 |
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| 1024x1024 | 0.49 | 0.48 | 10.6 | 5.08 | 4.06 |
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+--------------+---------+----------+-------+-------+---------+
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| 2048x2048 | 2.35 | 2.14 | 75.56 | 14.08 | 8.60 |
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| 2048x2048 | 1.92 | 1.86 | 52.7 | 13.90 | 8.50 |
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+--------------+---------+----------+-------+-------+---------+
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Additional Sources of Overhead

‎docs/source/user_guide/hardware/camera.rst‎

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.. _camera_configuration:
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=======
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Cameras
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=======
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The software supports camera-based acquisition. It can run both normal and rolling
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shutter modes of contemporary scientific CMOS cameras.
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Hamamatsu
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---------
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.. note::
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**navigate** has been tested with the following versions of the Hamamatsu's
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drivers:
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- DCAM API: 20.7.641, 21.7.4321, 22.9.6509, 22.11.4321, 23.12.6736
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- Camera Firmware: 2.21B, 2.53.A, 3.20.A, 4.30.B,
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- Active Silicon CoaXpress: 1.10, 1.13, 1.21.
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-----------------
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ORCA-Flash4.0 V3
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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- :ref:`Install Directions <dcam>`.
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- `ORCA-Flash 4.0 v3 Manual <https://www.hamamatsu
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.com/us/en/product/cameras/cmos-cameras/C13440-20CU.html>`_.
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.. collapse:: Configuration File
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.. code-block:: yaml
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microscopes:
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microscope_name:
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camera:
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hardware:
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type: HamamatsuOrca
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serial_number: 111
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camera_connection:
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defect_correct_mode: 2.0
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delay: 1.0 #ms
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settle_down: 0.1 #ms
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flip_x: False
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flip_y: False
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|
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------------------
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ORCA-Fusion
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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- :ref:`Install Directions <dcam>`.
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- `ORCA-Fusion Manual <https://www.hamamatsu
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.com/jp/en/product/cameras/cmos-cameras/C15440-20UP.html>`_.
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.. collapse:: Configuration File
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.. code-block:: yaml
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microscopes:
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microscope_name:
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camera:
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hardware:
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type: HamamatsuOrcaFusion
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serial_number: 111
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camera_connection:
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defect_correct_mode: 2.0
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delay: 1.0 #ms
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settle_down: 0.1 #ms
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flip_x: False
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flip_y: False
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|
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------------------
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ORCA-Lightning
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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- :ref:`Install Directions <dcam>`.
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- `ORCA-Lightning Manual <https://www.hamamatsu
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.com/us/en/product/cameras/cmos-cameras/C14120-20P.html>`_.
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.. collapse:: Configuration File
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.. code-block:: yaml
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microscopes:
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microscope_name:
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camera:
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hardware:
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type: HamamatsuOrcaLightning
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serial_number: 111
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camera_connection:
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defect_correct_mode: 2.0
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delay: 1.0 #ms
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settle_down: 0.1 #ms
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flip_x: False
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flip_y: False
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|
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------------------
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ORCA-Fire
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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- :ref:`Install Directions <dcam>`.
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- `ORCA-Fire Manual <https://www.hamamatsu.com/us/en/product/cameras/cmos-cameras/C16240-20UP.html>`_.
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.. collapse:: Configuration File
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.. code-block:: yaml
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microscopes:
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microscope_name:
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camera:
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hardware:
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type: HamamatsuOrcaFire
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serial_number: 111
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camera_connection:
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defect_correct_mode: 2.0
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delay: 1.0 #ms
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settle_down: 0.1 #ms
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flip_x: False
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flip_y: False
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|
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------------------
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Photometrics
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------------
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- :ref:`Install Directions <pvcam>`.
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.. note::
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**navigate** has been tested with the following versions of the Photometric's
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drivers:
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- PVCAM: 3.9.13
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-----------------
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Iris 15
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. collapse:: Configuration File
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.. code-block:: yaml
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microscopes:
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microscope_name:
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camera:
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hardware:
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type: Photometrics
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serial_number: 111
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camera_connection: PMPCIECam00
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defect_correct_mode: 2.0
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delay: 1.0 #ms
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settle_down: 0.1 #ms
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flip_x: False
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flip_y: False
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|
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------------------
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Synthetic Camera
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The synthetic camera simulates noise images from an sCMOS camera. If no camera is present,
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the synthetic camera class must be used.
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.. collapse:: Configuration File
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.. code-block:: yaml
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microscopes:
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microscope_name:
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camera:
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hardware:
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type: synthetic
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serial_number: 111
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camera_connection:
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defect_correct_mode: 2.0
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delay: 1.0 #ms
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settle_down: 0.1 #ms
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flip_x: False
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flip_y: False
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|

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