summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--.gitignore1
-rw-r--r--python-microeye.spec546
-rw-r--r--sources1
3 files changed, 548 insertions, 0 deletions
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 <Python_Bot@openeuler.org> - 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