From 5fb399c2bc193b639c0d8e2645ad75cfe66f2125 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Mon, 29 May 2023 11:14:13 +0000 Subject: automatic import of python-microeye --- .gitignore | 1 + python-microeye.spec | 546 +++++++++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 548 insertions(+) create mode 100644 python-microeye.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..5d42606 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/microEye-0.3.1.tar.gz diff --git a/python-microeye.spec b/python-microeye.spec new file mode 100644 index 0000000..0efb41f --- /dev/null +++ b/python-microeye.spec @@ -0,0 +1,546 @@ +%global _empty_manifest_terminate_build 0 +Name: python-microEye +Version: 0.3.1 +Release: 1 +Summary: A python toolkit for fluorescence microscopy that features industrial-grade CMOS cameras and Integrated Optics laser combiner MatchBox. +License: GNU General Public License v3 (GPLv3) +URL: https://github.com/samhitech/microEye +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/62/47/39e45f868c96e7d24f688e56dde21b355c7c9568926dea578fbd277bc738/microEye-0.3.1.tar.gz +BuildArch: noarch + + +%description +# microEye +A python toolkit for fluorescence microscopy that features IDS uEye industrial-grade CMOS cameras. + +The *Acquisition Module* allows multi-cam image acquisition within one graphical user interface. + +The *Control Module* allows setting the laser excitation presets, manual focus and automatic focus stabilization by monitoring the peak position of a totally internally reflected IR beam and moving the piezo stage accordingly. + +The *Tiff Viewer Module* allows accessing tiff images (single file and sequecnces) of order TYX (2D SMLM), also allows for visualizing the filtering-localization process *WYSIWYG*. + +This toolkit is compatible with the [hardware](#hardware) we are using in our microscope. For further details check our *miEye* microscope's [paper](https://doi.org/10.1016/j.ohx.2022.e00368) and [OSF project](http://doi.org/10.17605/osf.io/j2fqy). + +## Uses Packages + +- Numpy +- scipy +- pandas +- Zarr +- dask +- pyueye +- cv2 +- tifffile +- PyQt5 +- pyqtgraph +- qdarkstyle +- ome-types +- hidapi +- pyqode.python ([Jedi Fix](https://github.com/pyQode/pyqode.python/blob/6cc30087dab69d334a48c716d8d19fc1546ff0c6/pyqode/python/backend/workers.py)) +- VimbaPython (Included in [Vimba SDK](https://www.alliedvision.com/en/products/vimba-sdk/) and installed manually) + +## How to Install [Package](https://pypi.org/project/microEye/) + +1. Download and install the latest [*Python*](https://www.python.org/downloads/) 3.9 stable release. (We tested with 3.9.4 and 3.9.7) + +2. Open a terminal and install *microEye* package using *pip*. + + > pip install microEye + +3. Download the file [*requirements.txt*](https://github.com/samhitech/microEye/blob/main/requirements.txt) and install the *microEye* required packages by executing the following line. (This may take a while) + + > pip install -r /path/to/requirements.txt + +4. Install the dependent hardware specific drivers for the cameras if you intend to use the hardware control or acquisition modules. +(*microEye* might not function as expected in case drivers are missing) + * *Integrated Optics* [Laser control software](https://integratedoptics.com/downloads). + + * *IDS uEye* CMOS cameras: install [*IDS Software Suite 4.96.1*](https://en.ids-imaging.com/download-details/AB00604.html?os=windows&version=win10&bus=64&floatcalc=) for *Windows 32/64-bit*. (We did not test it with Linux) + + * *Allied Vision* CMOS cameras: install the [*Vimba SDK*](https://www.alliedvision.com/en/products/vimba-sdk) 5.0 or 6.0 outside the *Program Files* to skip the run as admin requirement, then in a terminal navigate to directory [*.../Allied Vision/Vimba_5.0/VimbaPython/*] where [*setup.py*] is located and execute: + + > python -m pip install . + + * *Thorlabs* CMOS cameras: install [Thorcam](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ThorCam) in its default directory as it is initial to have *uc480_64.dll* in path 'C:\Program Files\Thorlabs\Scientific Imaging\ThorCam\uc480_64.dll'. (Note, *Thorlabs* cameras can get identified by *Windows* as *IDS uEye* cameras and run without this software) + +5. Other hardware used by the *miEye* microscope include: + * *Thorlabs* [*Kinesis® Software*](https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=10285) and [*Elliptec™ Software*](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ELL). + +6. Download and run examples to start using *microEye*! :partying_face: + +## Microscope Scheme + +Schematic overview of the miEye instrument. A) The excitation path via single-mode fiber (SMF) for TIRF-, HILO-, and Epi-mode. B) The excitation path via multi-mode fiber (MMF) for Epi-mode when imaging MMF output on the sample plane. C) The fluorescence emission path. D) IR laser-based autofocusing path. AC: achromat lens, AS: aspheric lens, BFP: back-focal plane, TL: tube lens, B: B-coated N-BK7 optics, BS: beamsplitter. + +![quadScheme_4](https://user-images.githubusercontent.com/89871015/182302644-9fdf8615-75c3-4702-9913-d1a535f60e22.png) + +![scheme_git_0](https://user-images.githubusercontent.com/89871015/182302694-3f70d058-b1b6-4ef5-9cc2-aec9b58a05f0.png) + +## Hardware + +- Supported Cameras: + - IDS uEye industrial-grade CMOS cameras, specifically [UI-3060CP Rev. 2](https://en.ids-imaging.com/store/products/cameras/ui-3060cp-rev-2.html). + - Thorlabs DCx cameras using the UC480 driver, specifically [DCC1545M](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M). + - Allied Vision cameras using Vimba SDK, specifically [Alvium 1800 U-158m](https://www.alliedvision.com/en/products/alvium-configurator/alvium-1800-u/158/#_configurator). +- Integrated Optics Multi-wavelength Laser Combiner [MatchBox](https://integratedoptics.com/products/wavelength-combiners). +- Piezo Concept nanopositioner for microscope objectives [FOC](https://piezoconcept-store.squarespace.com/1-axis/p/foc). +- Thorlab's Elliptec Dual-Position/Four-Position ([ELL6](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL6)/[ELL9](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL9)) support. +- Thorlab's Kinesis [KDC101](https://www.thorlabs.com/thorproduct.cfm?partnumber=KDC101) controller for [Z825B](https://www.thorlabs.com/thorproduct.cfm?partnumber=Z825B) 25mm motorized actuators used for the XY stage instead of manual micrometers. (Requires activating USB VCP to access the COM port from device manger) +- Parallax Linescan Camera Module used for IR autofocus stabilization tracking [TSL1401-DB (#28317)](https://eu.mouser.com/ProductDetail/Parallax/28317?qs=%2Fha2pyFaduiCRhuOAXMuCmQIeG1Q3R01m6Y1EH%252BmN80%3D) acquisition done by an Arduino [LineScanner](https://github.com/samhitech/LineScanner). +- [RelayBox](https://github.com/samhitech/RelayBox) arduino for laser control using the camera flash signal with different presets. +- Parts list of our [miEye OSF Project](https://osf.io/j2fqy/) an iteration of [hohlbeinlab miCube](https://hohlbeinlab.github.io/miCube/index.html). + +## Acquisition Module + +![acquisition_module](https://user-images.githubusercontent.com/89871015/135764990-b9ac0062-4710-4a10-b2f8-a16f34d77ee1.png) + +### How to use + +For Vimba SDK to work the script should be executed as administrator on Windows and wrapped in a with statement: + + from microEye.hardware import acquisition_module + + try: + import vimba as vb + except Exception: + vb = None + + + if vb: + with vb.Vimba.get_instance() as vimba: + app, window = acquisition_module.StartGUI() + + app.exec_() + else: + app, window = acquisition_module.StartGUI() + + app.exec_() + +## Control Module + +![control_module](https://user-images.githubusercontent.com/89871015/141841883-d37c4979-c8aa-4e1f-b1b9-84bdd819c828.png) + +### How to use + + from microEye.hardware import control_module + + app, window = control_module.StartGUI() + app.exec_() + + +## miEye Module + +TBA + +## Data Viewer / Processor + +![Capture_viewer](https://user-images.githubusercontent.com/89871015/150964047-ba4521fa-1ffa-4f76-9e4e-6759fbdc3b8f.PNG) +![Capture_viewer_2](https://user-images.githubusercontent.com/89871015/150964062-9560b228-5052-40cb-86fc-5617f760a1b1.PNG) +![Capture_viewer_3](https://user-images.githubusercontent.com/89871015/151448086-0799926d-a4a4-420b-ad12-177145a90c78.png) + + +### How to use + + from microEye import tiff_viewer + + app, window = tiff_viewer.StartGUI('D:/') + + app.exec_() + + +## Authors + +Mohammad Nour Alsamsam + +[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/samhightech.svg?style=social&label=Follow%20%40samhightech)](https://twitter.com/samhightech) + +## People Involved + +Dr. Marijonas Tutkus (supervision) + +[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/MTutkus.svg?style=social&label=Follow%20%40MTutkus)](https://twitter.com/MTutkus) + + +Aurimas Kopūstas (sample preparation and experiments) + +## Acknowledgement + +![ack](https://user-images.githubusercontent.com/89871015/135897106-12656072-932e-45ea-abeb-54e86ba60eb0.png) + + + + +%package -n python3-microEye +Summary: A python toolkit for fluorescence microscopy that features industrial-grade CMOS cameras and Integrated Optics laser combiner MatchBox. +Provides: python-microEye +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-microEye +# microEye +A python toolkit for fluorescence microscopy that features IDS uEye industrial-grade CMOS cameras. + +The *Acquisition Module* allows multi-cam image acquisition within one graphical user interface. + +The *Control Module* allows setting the laser excitation presets, manual focus and automatic focus stabilization by monitoring the peak position of a totally internally reflected IR beam and moving the piezo stage accordingly. + +The *Tiff Viewer Module* allows accessing tiff images (single file and sequecnces) of order TYX (2D SMLM), also allows for visualizing the filtering-localization process *WYSIWYG*. + +This toolkit is compatible with the [hardware](#hardware) we are using in our microscope. For further details check our *miEye* microscope's [paper](https://doi.org/10.1016/j.ohx.2022.e00368) and [OSF project](http://doi.org/10.17605/osf.io/j2fqy). + +## Uses Packages + +- Numpy +- scipy +- pandas +- Zarr +- dask +- pyueye +- cv2 +- tifffile +- PyQt5 +- pyqtgraph +- qdarkstyle +- ome-types +- hidapi +- pyqode.python ([Jedi Fix](https://github.com/pyQode/pyqode.python/blob/6cc30087dab69d334a48c716d8d19fc1546ff0c6/pyqode/python/backend/workers.py)) +- VimbaPython (Included in [Vimba SDK](https://www.alliedvision.com/en/products/vimba-sdk/) and installed manually) + +## How to Install [Package](https://pypi.org/project/microEye/) + +1. Download and install the latest [*Python*](https://www.python.org/downloads/) 3.9 stable release. (We tested with 3.9.4 and 3.9.7) + +2. Open a terminal and install *microEye* package using *pip*. + + > pip install microEye + +3. Download the file [*requirements.txt*](https://github.com/samhitech/microEye/blob/main/requirements.txt) and install the *microEye* required packages by executing the following line. (This may take a while) + + > pip install -r /path/to/requirements.txt + +4. Install the dependent hardware specific drivers for the cameras if you intend to use the hardware control or acquisition modules. +(*microEye* might not function as expected in case drivers are missing) + * *Integrated Optics* [Laser control software](https://integratedoptics.com/downloads). + + * *IDS uEye* CMOS cameras: install [*IDS Software Suite 4.96.1*](https://en.ids-imaging.com/download-details/AB00604.html?os=windows&version=win10&bus=64&floatcalc=) for *Windows 32/64-bit*. (We did not test it with Linux) + + * *Allied Vision* CMOS cameras: install the [*Vimba SDK*](https://www.alliedvision.com/en/products/vimba-sdk) 5.0 or 6.0 outside the *Program Files* to skip the run as admin requirement, then in a terminal navigate to directory [*.../Allied Vision/Vimba_5.0/VimbaPython/*] where [*setup.py*] is located and execute: + + > python -m pip install . + + * *Thorlabs* CMOS cameras: install [Thorcam](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ThorCam) in its default directory as it is initial to have *uc480_64.dll* in path 'C:\Program Files\Thorlabs\Scientific Imaging\ThorCam\uc480_64.dll'. (Note, *Thorlabs* cameras can get identified by *Windows* as *IDS uEye* cameras and run without this software) + +5. Other hardware used by the *miEye* microscope include: + * *Thorlabs* [*Kinesis® Software*](https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=10285) and [*Elliptec™ Software*](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ELL). + +6. Download and run examples to start using *microEye*! :partying_face: + +## Microscope Scheme + +Schematic overview of the miEye instrument. A) The excitation path via single-mode fiber (SMF) for TIRF-, HILO-, and Epi-mode. B) The excitation path via multi-mode fiber (MMF) for Epi-mode when imaging MMF output on the sample plane. C) The fluorescence emission path. D) IR laser-based autofocusing path. AC: achromat lens, AS: aspheric lens, BFP: back-focal plane, TL: tube lens, B: B-coated N-BK7 optics, BS: beamsplitter. + +![quadScheme_4](https://user-images.githubusercontent.com/89871015/182302644-9fdf8615-75c3-4702-9913-d1a535f60e22.png) + +![scheme_git_0](https://user-images.githubusercontent.com/89871015/182302694-3f70d058-b1b6-4ef5-9cc2-aec9b58a05f0.png) + +## Hardware + +- Supported Cameras: + - IDS uEye industrial-grade CMOS cameras, specifically [UI-3060CP Rev. 2](https://en.ids-imaging.com/store/products/cameras/ui-3060cp-rev-2.html). + - Thorlabs DCx cameras using the UC480 driver, specifically [DCC1545M](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M). + - Allied Vision cameras using Vimba SDK, specifically [Alvium 1800 U-158m](https://www.alliedvision.com/en/products/alvium-configurator/alvium-1800-u/158/#_configurator). +- Integrated Optics Multi-wavelength Laser Combiner [MatchBox](https://integratedoptics.com/products/wavelength-combiners). +- Piezo Concept nanopositioner for microscope objectives [FOC](https://piezoconcept-store.squarespace.com/1-axis/p/foc). +- Thorlab's Elliptec Dual-Position/Four-Position ([ELL6](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL6)/[ELL9](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL9)) support. +- Thorlab's Kinesis [KDC101](https://www.thorlabs.com/thorproduct.cfm?partnumber=KDC101) controller for [Z825B](https://www.thorlabs.com/thorproduct.cfm?partnumber=Z825B) 25mm motorized actuators used for the XY stage instead of manual micrometers. (Requires activating USB VCP to access the COM port from device manger) +- Parallax Linescan Camera Module used for IR autofocus stabilization tracking [TSL1401-DB (#28317)](https://eu.mouser.com/ProductDetail/Parallax/28317?qs=%2Fha2pyFaduiCRhuOAXMuCmQIeG1Q3R01m6Y1EH%252BmN80%3D) acquisition done by an Arduino [LineScanner](https://github.com/samhitech/LineScanner). +- [RelayBox](https://github.com/samhitech/RelayBox) arduino for laser control using the camera flash signal with different presets. +- Parts list of our [miEye OSF Project](https://osf.io/j2fqy/) an iteration of [hohlbeinlab miCube](https://hohlbeinlab.github.io/miCube/index.html). + +## Acquisition Module + +![acquisition_module](https://user-images.githubusercontent.com/89871015/135764990-b9ac0062-4710-4a10-b2f8-a16f34d77ee1.png) + +### How to use + +For Vimba SDK to work the script should be executed as administrator on Windows and wrapped in a with statement: + + from microEye.hardware import acquisition_module + + try: + import vimba as vb + except Exception: + vb = None + + + if vb: + with vb.Vimba.get_instance() as vimba: + app, window = acquisition_module.StartGUI() + + app.exec_() + else: + app, window = acquisition_module.StartGUI() + + app.exec_() + +## Control Module + +![control_module](https://user-images.githubusercontent.com/89871015/141841883-d37c4979-c8aa-4e1f-b1b9-84bdd819c828.png) + +### How to use + + from microEye.hardware import control_module + + app, window = control_module.StartGUI() + app.exec_() + + +## miEye Module + +TBA + +## Data Viewer / Processor + +![Capture_viewer](https://user-images.githubusercontent.com/89871015/150964047-ba4521fa-1ffa-4f76-9e4e-6759fbdc3b8f.PNG) +![Capture_viewer_2](https://user-images.githubusercontent.com/89871015/150964062-9560b228-5052-40cb-86fc-5617f760a1b1.PNG) +![Capture_viewer_3](https://user-images.githubusercontent.com/89871015/151448086-0799926d-a4a4-420b-ad12-177145a90c78.png) + + +### How to use + + from microEye import tiff_viewer + + app, window = tiff_viewer.StartGUI('D:/') + + app.exec_() + + +## Authors + +Mohammad Nour Alsamsam + +[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/samhightech.svg?style=social&label=Follow%20%40samhightech)](https://twitter.com/samhightech) + +## People Involved + +Dr. Marijonas Tutkus (supervision) + +[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/MTutkus.svg?style=social&label=Follow%20%40MTutkus)](https://twitter.com/MTutkus) + + +Aurimas Kopūstas (sample preparation and experiments) + +## Acknowledgement + +![ack](https://user-images.githubusercontent.com/89871015/135897106-12656072-932e-45ea-abeb-54e86ba60eb0.png) + + + + +%package help +Summary: Development documents and examples for microEye +Provides: python3-microEye-doc +%description help +# microEye +A python toolkit for fluorescence microscopy that features IDS uEye industrial-grade CMOS cameras. + +The *Acquisition Module* allows multi-cam image acquisition within one graphical user interface. + +The *Control Module* allows setting the laser excitation presets, manual focus and automatic focus stabilization by monitoring the peak position of a totally internally reflected IR beam and moving the piezo stage accordingly. + +The *Tiff Viewer Module* allows accessing tiff images (single file and sequecnces) of order TYX (2D SMLM), also allows for visualizing the filtering-localization process *WYSIWYG*. + +This toolkit is compatible with the [hardware](#hardware) we are using in our microscope. For further details check our *miEye* microscope's [paper](https://doi.org/10.1016/j.ohx.2022.e00368) and [OSF project](http://doi.org/10.17605/osf.io/j2fqy). + +## Uses Packages + +- Numpy +- scipy +- pandas +- Zarr +- dask +- pyueye +- cv2 +- tifffile +- PyQt5 +- pyqtgraph +- qdarkstyle +- ome-types +- hidapi +- pyqode.python ([Jedi Fix](https://github.com/pyQode/pyqode.python/blob/6cc30087dab69d334a48c716d8d19fc1546ff0c6/pyqode/python/backend/workers.py)) +- VimbaPython (Included in [Vimba SDK](https://www.alliedvision.com/en/products/vimba-sdk/) and installed manually) + +## How to Install [Package](https://pypi.org/project/microEye/) + +1. Download and install the latest [*Python*](https://www.python.org/downloads/) 3.9 stable release. (We tested with 3.9.4 and 3.9.7) + +2. Open a terminal and install *microEye* package using *pip*. + + > pip install microEye + +3. Download the file [*requirements.txt*](https://github.com/samhitech/microEye/blob/main/requirements.txt) and install the *microEye* required packages by executing the following line. (This may take a while) + + > pip install -r /path/to/requirements.txt + +4. Install the dependent hardware specific drivers for the cameras if you intend to use the hardware control or acquisition modules. +(*microEye* might not function as expected in case drivers are missing) + * *Integrated Optics* [Laser control software](https://integratedoptics.com/downloads). + + * *IDS uEye* CMOS cameras: install [*IDS Software Suite 4.96.1*](https://en.ids-imaging.com/download-details/AB00604.html?os=windows&version=win10&bus=64&floatcalc=) for *Windows 32/64-bit*. (We did not test it with Linux) + + * *Allied Vision* CMOS cameras: install the [*Vimba SDK*](https://www.alliedvision.com/en/products/vimba-sdk) 5.0 or 6.0 outside the *Program Files* to skip the run as admin requirement, then in a terminal navigate to directory [*.../Allied Vision/Vimba_5.0/VimbaPython/*] where [*setup.py*] is located and execute: + + > python -m pip install . + + * *Thorlabs* CMOS cameras: install [Thorcam](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ThorCam) in its default directory as it is initial to have *uc480_64.dll* in path 'C:\Program Files\Thorlabs\Scientific Imaging\ThorCam\uc480_64.dll'. (Note, *Thorlabs* cameras can get identified by *Windows* as *IDS uEye* cameras and run without this software) + +5. Other hardware used by the *miEye* microscope include: + * *Thorlabs* [*Kinesis® Software*](https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=10285) and [*Elliptec™ Software*](https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ELL). + +6. Download and run examples to start using *microEye*! :partying_face: + +## Microscope Scheme + +Schematic overview of the miEye instrument. A) The excitation path via single-mode fiber (SMF) for TIRF-, HILO-, and Epi-mode. B) The excitation path via multi-mode fiber (MMF) for Epi-mode when imaging MMF output on the sample plane. C) The fluorescence emission path. D) IR laser-based autofocusing path. AC: achromat lens, AS: aspheric lens, BFP: back-focal plane, TL: tube lens, B: B-coated N-BK7 optics, BS: beamsplitter. + +![quadScheme_4](https://user-images.githubusercontent.com/89871015/182302644-9fdf8615-75c3-4702-9913-d1a535f60e22.png) + +![scheme_git_0](https://user-images.githubusercontent.com/89871015/182302694-3f70d058-b1b6-4ef5-9cc2-aec9b58a05f0.png) + +## Hardware + +- Supported Cameras: + - IDS uEye industrial-grade CMOS cameras, specifically [UI-3060CP Rev. 2](https://en.ids-imaging.com/store/products/cameras/ui-3060cp-rev-2.html). + - Thorlabs DCx cameras using the UC480 driver, specifically [DCC1545M](https://www.thorlabs.com/thorProduct.cfm?partNumber=DCC1545M). + - Allied Vision cameras using Vimba SDK, specifically [Alvium 1800 U-158m](https://www.alliedvision.com/en/products/alvium-configurator/alvium-1800-u/158/#_configurator). +- Integrated Optics Multi-wavelength Laser Combiner [MatchBox](https://integratedoptics.com/products/wavelength-combiners). +- Piezo Concept nanopositioner for microscope objectives [FOC](https://piezoconcept-store.squarespace.com/1-axis/p/foc). +- Thorlab's Elliptec Dual-Position/Four-Position ([ELL6](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL6)/[ELL9](https://www.thorlabs.com/thorproduct.cfm?partnumber=ELL9)) support. +- Thorlab's Kinesis [KDC101](https://www.thorlabs.com/thorproduct.cfm?partnumber=KDC101) controller for [Z825B](https://www.thorlabs.com/thorproduct.cfm?partnumber=Z825B) 25mm motorized actuators used for the XY stage instead of manual micrometers. (Requires activating USB VCP to access the COM port from device manger) +- Parallax Linescan Camera Module used for IR autofocus stabilization tracking [TSL1401-DB (#28317)](https://eu.mouser.com/ProductDetail/Parallax/28317?qs=%2Fha2pyFaduiCRhuOAXMuCmQIeG1Q3R01m6Y1EH%252BmN80%3D) acquisition done by an Arduino [LineScanner](https://github.com/samhitech/LineScanner). +- [RelayBox](https://github.com/samhitech/RelayBox) arduino for laser control using the camera flash signal with different presets. +- Parts list of our [miEye OSF Project](https://osf.io/j2fqy/) an iteration of [hohlbeinlab miCube](https://hohlbeinlab.github.io/miCube/index.html). + +## Acquisition Module + +![acquisition_module](https://user-images.githubusercontent.com/89871015/135764990-b9ac0062-4710-4a10-b2f8-a16f34d77ee1.png) + +### How to use + +For Vimba SDK to work the script should be executed as administrator on Windows and wrapped in a with statement: + + from microEye.hardware import acquisition_module + + try: + import vimba as vb + except Exception: + vb = None + + + if vb: + with vb.Vimba.get_instance() as vimba: + app, window = acquisition_module.StartGUI() + + app.exec_() + else: + app, window = acquisition_module.StartGUI() + + app.exec_() + +## Control Module + +![control_module](https://user-images.githubusercontent.com/89871015/141841883-d37c4979-c8aa-4e1f-b1b9-84bdd819c828.png) + +### How to use + + from microEye.hardware import control_module + + app, window = control_module.StartGUI() + app.exec_() + + +## miEye Module + +TBA + +## Data Viewer / Processor + +![Capture_viewer](https://user-images.githubusercontent.com/89871015/150964047-ba4521fa-1ffa-4f76-9e4e-6759fbdc3b8f.PNG) +![Capture_viewer_2](https://user-images.githubusercontent.com/89871015/150964062-9560b228-5052-40cb-86fc-5617f760a1b1.PNG) +![Capture_viewer_3](https://user-images.githubusercontent.com/89871015/151448086-0799926d-a4a4-420b-ad12-177145a90c78.png) + + +### How to use + + from microEye import tiff_viewer + + app, window = tiff_viewer.StartGUI('D:/') + + app.exec_() + + +## Authors + +Mohammad Nour Alsamsam + +[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/samhightech.svg?style=social&label=Follow%20%40samhightech)](https://twitter.com/samhightech) + +## People Involved + +Dr. Marijonas Tutkus (supervision) + +[![Twitter URL](https://img.shields.io/twitter/url/https/twitter.com/MTutkus.svg?style=social&label=Follow%20%40MTutkus)](https://twitter.com/MTutkus) + + +Aurimas Kopūstas (sample preparation and experiments) + +## Acknowledgement + +![ack](https://user-images.githubusercontent.com/89871015/135897106-12656072-932e-45ea-abeb-54e86ba60eb0.png) + + + + +%prep +%autosetup -n microEye-0.3.1 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-microEye -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 29 2023 Python_Bot - 0.3.1-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..0eb4d39 --- /dev/null +++ b/sources @@ -0,0 +1 @@ +5250dff2757803d61a87184247f802f6 microEye-0.3.1.tar.gz -- cgit v1.2.3