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|
%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.aliyun.com/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.
## 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
### 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
### How to use
from microEye.hardware import control_module
app, window = control_module.StartGUI()
app.exec_()
## miEye Module
TBA
## Data Viewer / Processor
### How to use
from microEye import tiff_viewer
app, window = tiff_viewer.StartGUI('D:/')
app.exec_()
## Authors
Mohammad Nour Alsamsam
[](https://twitter.com/samhightech)
## People Involved
Dr. Marijonas Tutkus (supervision)
[](https://twitter.com/MTutkus)
Aurimas Kopūstas (sample preparation and experiments)
## Acknowledgement
%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.
## 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
### 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
### How to use
from microEye.hardware import control_module
app, window = control_module.StartGUI()
app.exec_()
## miEye Module
TBA
## Data Viewer / Processor
### How to use
from microEye import tiff_viewer
app, window = tiff_viewer.StartGUI('D:/')
app.exec_()
## Authors
Mohammad Nour Alsamsam
[](https://twitter.com/samhightech)
## People Involved
Dr. Marijonas Tutkus (supervision)
[](https://twitter.com/MTutkus)
Aurimas Kopūstas (sample preparation and experiments)
## Acknowledgement
%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.
## 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
### 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
### How to use
from microEye.hardware import control_module
app, window = control_module.StartGUI()
app.exec_()
## miEye Module
TBA
## Data Viewer / Processor
### How to use
from microEye import tiff_viewer
app, window = tiff_viewer.StartGUI('D:/')
app.exec_()
## Authors
Mohammad Nour Alsamsam
[](https://twitter.com/samhightech)
## People Involved
Dr. Marijonas Tutkus (supervision)
[](https://twitter.com/MTutkus)
Aurimas Kopūstas (sample preparation and experiments)
## Acknowledgement
%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
* Fri Jun 09 2023 Python_Bot <Python_Bot@openeuler.org> - 0.3.1-1
- Package Spec generated
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