[](https://pepy.tech/project/AxionVueOpenAPI)
[](https://pepy.tech/project/CytoSmartOpenAPI)
[](https://pepy.tech/project/luxconnector)
# Axion Vue Open API
This is a Python wrapper for the Axion Vue Windows app to use it headless.
The package will only work on Windows 10 and above.
This package was formally known as `luxconnector`
## Warranty
> ⚠️ **Hardware warranty is void by using this open API** ⚠️:
>
> Using the AxionVueOpenAPI means you will have NO hardware warranty (see license).
This is because our devices are made to handle the normal usage ([the GUI app](https://download.axionbio.com/)).
It also includes additionally bought warranty.
Only if your additionally bought warranty implicitly includes the Open API usage you will have warranty.
## Installation
To install this package follow these steps:
### Step 1: Drivers
Make sure you had a [Axion Vue application installed](http://download.axionbio.com/).
Recommended is the cell counter given it does not restart itself after closing.
This is needed to have all the correct drivers installed.
Uninstall the app afterwards.
If the app is on the same machine the Open API might connect with the wrong one.
### Step 2: pip install
```cmd
pip install AxionVueOpenAPI
```
## Initialization
Make sure at least one Axion imaging device is physically connected to your computer via a USB3 port.
The AxionVueOpenAPI is an object that maintains the connection with the device.
To create the object use the following code:
```python
from AxionVueOpenAPI import AxionVueOpenAPI
connector = AxionVueOpenAPI(number_of_devices=2, warranty=False)
```
> ⚠️ You are voiding your warranty by using this package
NOTE: Make sure number_of_devices does not exceed the number of devices you have physically connected.
Otherwise the AxionVueOpenAPI will look for the missing devices forever.
## Getting serial numbers
Each physical device has a serial number.
This number is needed to send commands to a specific device.
```python
serial_numbers = connector.get_all_serial_numbers()
```
## Getting a single image
When you want a single image taken at this moment use get_image.
This will return the image as a [`pillow image`](https://pillow.readthedocs.io/en/stable/reference/Image.html).
You need to give the serial number of the device you want to target.
```python
img = connector.get_image(serial_number)
```
or
```python
img = connector.get_image(serial_numbers[index])
```
## Changing the focus
This function will change the focus for the AxionVueOpenAPI object.
Every image taken after this function will have the new focus.
The focus is in the range 0 until 1. (0.0 and 1.0 are valid entries)
You need to give the serial number of the device you want to target.
```python
connector.set_focus(serial_number, 0.5)
img1 = connector.get_image(serial_number) # Image with focus of 0.5
connector.set_focus(serial_number, 0.7)
img2 = connector.get_image(serial_number) # Image with focus of 0.7
img3 = connector.get_image(serial_number) # Image with focus of 0.7
```
## Auto focus
The device goes over multiple possible focuses to find the best focus.
It will use image analysis to determine how well the image is in focus.
```python
# Fast but goes over a limited range to cover most manufactured cell counting slides
connector.do_autofocus(serial_number, "slide")
# Fastest: goes over the limited range where cells can be in focus on the Axion Exact slide
connector.do_autofocus(serial_number, "CSslide")
# Slow, but goes over the full range of possible focusses: suitable for any vessel that works with the Axion imaging device
connector.do_autofocus(serial_number, "other")
```
## Getting the temperature
This function returns the temperature in Celsius of the device.
You need to give the serial number of the device you want to target.
```python
temperature = connector.get_temperature(serial_number)
```
## Change active camera (fluorescence)
To use fluorescence you will need to change the active camera.
The camera can be set to 3 different values, RED, GREEN, or BRIGHTFIELD.
This will only work if your device is an FL device otherwise only BRIGHTFIELD is available.
```python
connector.set_active_camera(serial_number, "RED")
connector.set_active_camera(serial_number, "GREEN")
connector.set_active_camera(serial_number, "BRIGHTFIELD")
```
## Change camera setting
Each camera has its own settings.
Not all settings are available for BRIGHTFIELD.
- exposure: The time in milliseconds that the camera is detecting light. (Lux and Exact devices only; for Omni devices use flash duration)
- gain: The multiplication of the camera. (Fluo only)
If very little light goes into the camera sensor make sure the gain is high.
- brightness: Strength of the led when it is on. (Fluo only)
- focus_offset: The difference in focus between brightfield and fluo.
If focus is set to 0.4 and focus_offset for RED is set to 0.1 RED focus is 0.5 (Fluo only)
```python
connector.set_camera_settings(serial_number, "RED", 500, gain=30, brightness=5000, focus_offset=0.0)
connector.set_camera_settings(serial_number, "BRIGHTFIELD", 10)
```
## Change flash duration (Omni only)
The Omni cannot change the exposure time but can change the time the led is on.
This can be done with set_flash_duration.
It will set the duration between 40 and 250 μs.
```python
connector.set_flash_duration(serial_number, duration=120)
```
If you do NOT have an Omni use set_camera_settings.
## Getting a z-stack
This function will return a list of [`pillow images`](https://pillow.readthedocs.io/en/stable/reference/Image.html).
Each image will be at a different focus level.
This code will create a z-stack of 6 images.
The focuses of these images will be [0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
You need to give the serial number of the device you want to target.
```python
list_of_imgs = connector.get_z_stack(serial_number, num_img = 6, start_focus = 0.5, stop_focus = 1)
```
## Change stage (Omni only)
To change the position of the Omni stage (camera, led, arm, ect.) give the new position in mm.
- Position x in mm
- Position y in mm
- Time in seconds it can wait till it arrives (default 60)
```python
connector.move_stage(serial_number, 100, 100, 60)
```
After this the normal process for obtaining and changing cameras applies.
## Get stage position (Omni only)
If you need to know where the stage is, use get_position.
This also works if the Omni moved without a move_stage command (e.g. when it goes to sleep).
```python
print(connector.get_position(serial_number))
```
## Changing zoom modes (Lux only)
There are 2 zoom modes: "IN" and "OUT".
While zoomed in the resolution is higher but the ROI is smaller, zoomed out has a higher ROI but a lower resolution.
Since zooming in comprises digital zoom, the image will not show more sample details.
Changing this setting will change it for every image or z-stack taken afterwards.
You need to give the serial number of the device you want to target.
```python
connector.set_zoom(serial_number, "IN")
img1 = connector.get_image(serial_number) # Image is zoomed in
connector.set_zoom(serial_number, "OUT")
img2 = connector.get_image(serial_number) # Image is zoomed out
```
## Live view
The live view of the device is hosted at http://localhost:3333/cytosmartservice/live?serialNumber=##########.
This image can only been seen if the live view is turned on (by default the live view is turned on).
You need to give the serial number of the device you want to target at the place of the #-symbols.
```python
connector.set_liveview(serial_number, False) # Led of device turns off till you take a picture
connector.set_liveview(serial_number, True) # In the browser you can see the image being updated
connector.open_liveview(serial_number) # Opens liveview in the default browser
```
## Developers
Developers of the AxionVueOpenAPI please look at the [`developers readme`](README_DEV.md)
## Credits
- Tom "RoadRunner" Nijhof
- Nora
- Tessa
- Marc "it is with a c" van Vijven
- Julia "I did not break it, I tested it" van den Beemd
- Count Nicolai Vondracek, Señior sunshine manager
History
-------
1.3.1 (2023-03-29)
------------------
- Renaming to AxionVueOpenAPI
1.3.0 (2022-08-25)
------------------
- Add open_liveview
- Add do_autofocus
- Add listener to autofocus change
- Bugfix: set_focus. Make sure camera_setting is completed before setting the focus
1.2.0 (2022-06-27)
------------------
- Update server to support Omni
- Add move stage
- Add get position
- Add set flash duration
- Add mandatory turning off of warranty
- Check for connection loss and reconnect is closed
- Check for sleeping device
1.1.1 (2022-06-29)
------------------
- Update documentation
1.1.0 (2021-12-03)
------------------
- Add change camera settings
- Add set activate camera (brightfield, red-fluo, or green-fluo)
- Change focus:
make sure focus always happens in brightfield camera mode
Add sleep after changing to focus so camera can move to new position
- Update to new Cytosmart app
1.0.4 (2021-04-15)
------------------
- Update Pillow
- Fix installation requirements
1.0.3 (2021-11-22)
------------------
- Update requirements of websocket and websocket-client to include version 1
- Check if app is open before starting a new one
1.0.2 (2021-04-15)
------------------
- Update pillow
- Update license to ACADEMIC PUBLIC LICENSE
1.0.1 (2021-01-14)
------------------
- Added support for LUX3 FL
- Bugfix: toggle liveview when change zoom level
1.0.0 (2020-09-15)
------------------
- Added multi lux support
- Changed output from numpy array to pillow
- Require serial number with function to get information
- Add get_temperature
0.1.2 (2020-06-30)
------------------
- Rename failing to pinging in print statement
0.1.1 (2020-06-11)
------------------
- Update documentation
- Make setup.py fit for PyPI
0.1.0 (2020-05-20)
------------------
- Update lux server to latest version
0.0.3 (2020-03-30)
------------------
- bugfix: files were not copied into package on linux
0.0.2 (2020-03-24)
------------------
- Bugfix: stop waiting for response after sending a message
0.0.1 (2020-03-16)
------------------
- Add function: Copy the luxconnector
- Add function: focus change option
- Add function: z-stack
- Bugfix: add lux app to manifest
0.0.0 (2020-03-13)
------------------
Copied basic package a start of luxconnector
ACADEMIC PUBLIC LICENSE
version 1.1
Copyright (C) 2021
Preamble
This license contains the terms and conditions of using AxionVueOpenAPI in
noncommercial settings: at academic institutions for teaching and research
use and for personal or educational purposes. You will find that this
license provides noncommercial users of AxionVueOpenAPI with rights that are
similar to the well-known GNU General Public License, yet it retains the
possibility for AxionVueOpenAPI authors to financially support the development by
selling commercial licenses. In fact, if you intend to use AxionVueOpenAPI in a
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research projects, then you need to obtain a commercial license.
In that case, or if you are unsure, please contact the Author imaging.support@axionbio.com
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What are the rights given to noncommercial users? Similarly to GPL, you
have the right to use the software, to distribute copies, to receive source
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We believe that the combination of noncommercial open-source and commercial
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commercial licenses will enable faster development and a higher level of
software quality, while further enjoying the informal, open communication
and collaboration channels of open source development.
The precise terms and conditions for using, copying, distribution and
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END OF TERMS AND CONDITIONS
Initially written by Andras Varga (public domain) for OMNeT++ https://omnetpp.org/intro/license,
adapted by CytoSMART TECHNOLOGIES BV. The adaptation is licensed under CC0 1.0 (Public Domain Dedication).
Raw data
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"description": "[](https://pepy.tech/project/AxionVueOpenAPI)\n[](https://pepy.tech/project/CytoSmartOpenAPI)\n[](https://pepy.tech/project/luxconnector)\n\n# Axion Vue Open API\n\nThis is a Python wrapper for the Axion Vue Windows app to use it headless.\nThe package will only work on Windows 10 and above.\n\nThis package was formally known as `luxconnector`\n\n## Warranty\n\n> \u26a0\ufe0f **Hardware warranty is void by using this open API** \u26a0\ufe0f:\n>\n> Using the AxionVueOpenAPI means you will have NO hardware warranty (see license).\n\nThis is because our devices are made to handle the normal usage ([the GUI app](https://download.axionbio.com/)).\nIt also includes additionally bought warranty.\nOnly if your additionally bought warranty implicitly includes the Open API usage you will have warranty.\n\n## Installation\n\nTo install this package follow these steps:\n\n### Step 1: Drivers\n\nMake sure you had a [Axion Vue application installed](http://download.axionbio.com/).\n\nRecommended is the cell counter given it does not restart itself after closing.\nThis is needed to have all the correct drivers installed.\nUninstall the app afterwards.\nIf the app is on the same machine the Open API might connect with the wrong one.\n\n### Step 2: pip install\n\n```cmd\npip install AxionVueOpenAPI\n```\n\n## Initialization\n\nMake sure at least one Axion imaging device is physically connected to your computer via a USB3 port.\nThe AxionVueOpenAPI is an object that maintains the connection with the device.\nTo create the object use the following code:\n\n```python\nfrom AxionVueOpenAPI import AxionVueOpenAPI\nconnector = AxionVueOpenAPI(number_of_devices=2, warranty=False)\n```\n\n> \u26a0\ufe0f You are voiding your warranty by using this package\n\nNOTE: Make sure number_of_devices does not exceed the number of devices you have physically connected.\nOtherwise the AxionVueOpenAPI will look for the missing devices forever.\n\n## Getting serial numbers\n\nEach physical device has a serial number.\nThis number is needed to send commands to a specific device.\n\n```python\nserial_numbers = connector.get_all_serial_numbers()\n```\n\n## Getting a single image\n\nWhen you want a single image taken at this moment use get_image.\nThis will return the image as a [`pillow image`](https://pillow.readthedocs.io/en/stable/reference/Image.html).\nYou need to give the serial number of the device you want to target.\n\n```python\nimg = connector.get_image(serial_number)\n```\n\nor\n\n```python\nimg = connector.get_image(serial_numbers[index])\n```\n\n## Changing the focus\n\nThis function will change the focus for the AxionVueOpenAPI object.\nEvery image taken after this function will have the new focus.\n\nThe focus is in the range 0 until 1. (0.0 and 1.0 are valid entries)\n\nYou need to give the serial number of the device you want to target.\n\n```python\nconnector.set_focus(serial_number, 0.5)\nimg1 = connector.get_image(serial_number) # Image with focus of 0.5\nconnector.set_focus(serial_number, 0.7)\nimg2 = connector.get_image(serial_number) # Image with focus of 0.7\nimg3 = connector.get_image(serial_number) # Image with focus of 0.7\n```\n\n## Auto focus\n\nThe device goes over multiple possible focuses to find the best focus.\nIt will use image analysis to determine how well the image is in focus.\n\n```python\n# Fast but goes over a limited range to cover most manufactured cell counting slides\nconnector.do_autofocus(serial_number, \"slide\")\n# Fastest: goes over the limited range where cells can be in focus on the Axion Exact slide\nconnector.do_autofocus(serial_number, \"CSslide\")\n# Slow, but goes over the full range of possible focusses: suitable for any vessel that works with the Axion imaging device\nconnector.do_autofocus(serial_number, \"other\")\n```\n\n## Getting the temperature\n\nThis function returns the temperature in Celsius of the device.\n\nYou need to give the serial number of the device you want to target.\n\n```python\ntemperature = connector.get_temperature(serial_number)\n```\n\n## Change active camera (fluorescence)\n\nTo use fluorescence you will need to change the active camera.\nThe camera can be set to 3 different values, RED, GREEN, or BRIGHTFIELD.\nThis will only work if your device is an FL device otherwise only BRIGHTFIELD is available.\n\n```python\nconnector.set_active_camera(serial_number, \"RED\")\nconnector.set_active_camera(serial_number, \"GREEN\")\nconnector.set_active_camera(serial_number, \"BRIGHTFIELD\")\n```\n\n## Change camera setting\n\nEach camera has its own settings.\nNot all settings are available for BRIGHTFIELD.\n\n- exposure: The time in milliseconds that the camera is detecting light. (Lux and Exact devices only; for Omni devices use flash duration)\n- gain: The multiplication of the camera. (Fluo only)\n If very little light goes into the camera sensor make sure the gain is high.\n- brightness: Strength of the led when it is on. (Fluo only)\n- focus_offset: The difference in focus between brightfield and fluo.\n If focus is set to 0.4 and focus_offset for RED is set to 0.1 RED focus is 0.5 (Fluo only)\n\n```python\nconnector.set_camera_settings(serial_number, \"RED\", 500, gain=30, brightness=5000, focus_offset=0.0)\nconnector.set_camera_settings(serial_number, \"BRIGHTFIELD\", 10)\n```\n\n## Change flash duration (Omni only)\n\nThe Omni cannot change the exposure time but can change the time the led is on.\nThis can be done with set_flash_duration.\nIt will set the duration between 40 and 250 \u03bcs.\n\n```python\nconnector.set_flash_duration(serial_number, duration=120)\n```\n\nIf you do NOT have an Omni use set_camera_settings.\n\n## Getting a z-stack\n\nThis function will return a list of [`pillow images`](https://pillow.readthedocs.io/en/stable/reference/Image.html).\nEach image will be at a different focus level.\n\nThis code will create a z-stack of 6 images.\nThe focuses of these images will be [0.5, 0.6, 0.7, 0.8, 0.9, 1.0]\n\nYou need to give the serial number of the device you want to target.\n\n```python\nlist_of_imgs = connector.get_z_stack(serial_number, num_img = 6, start_focus = 0.5, stop_focus = 1)\n```\n\n## Change stage (Omni only)\n\nTo change the position of the Omni stage (camera, led, arm, ect.) give the new position in mm.\n\n- Position x in mm\n- Position y in mm\n- Time in seconds it can wait till it arrives (default 60)\n\n```python\nconnector.move_stage(serial_number, 100, 100, 60)\n```\n\nAfter this the normal process for obtaining and changing cameras applies.\n\n## Get stage position (Omni only)\n\nIf you need to know where the stage is, use get_position.\nThis also works if the Omni moved without a move_stage command (e.g. when it goes to sleep).\n\n```python\nprint(connector.get_position(serial_number))\n```\n\n## Changing zoom modes (Lux only)\n\nThere are 2 zoom modes: \"IN\" and \"OUT\".\nWhile zoomed in the resolution is higher but the ROI is smaller, zoomed out has a higher ROI but a lower resolution.\nSince zooming in comprises digital zoom, the image will not show more sample details.\n\nChanging this setting will change it for every image or z-stack taken afterwards.\n\nYou need to give the serial number of the device you want to target.\n\n```python\nconnector.set_zoom(serial_number, \"IN\")\nimg1 = connector.get_image(serial_number) # Image is zoomed in\nconnector.set_zoom(serial_number, \"OUT\")\nimg2 = connector.get_image(serial_number) # Image is zoomed out\n```\n\n## Live view\n\nThe live view of the device is hosted at http://localhost:3333/cytosmartservice/live?serialNumber=##########.\nThis image can only been seen if the live view is turned on (by default the live view is turned on).\n\nYou need to give the serial number of the device you want to target at the place of the #-symbols.\n\n```python\nconnector.set_liveview(serial_number, False) # Led of device turns off till you take a picture\nconnector.set_liveview(serial_number, True) # In the browser you can see the image being updated\nconnector.open_liveview(serial_number) # Opens liveview in the default browser\n```\n\n## Developers\n\nDevelopers of the AxionVueOpenAPI please look at the [`developers readme`](README_DEV.md)\n\n## Credits\n\n- Tom \"RoadRunner\" Nijhof\n- Nora\n- Tessa\n- Marc \"it is with a c\" van Vijven\n- Julia \"I did not break it, I tested it\" van den Beemd\n- Count Nicolai Vondracek, Se\u00f1ior sunshine manager\n\n\nHistory\n-------\n1.3.1 (2023-03-29)\n------------------\n- Renaming to AxionVueOpenAPI\n\n1.3.0 (2022-08-25)\n------------------\n- Add open_liveview\n- Add do_autofocus\n- Add listener to autofocus change\n- Bugfix: set_focus. Make sure camera_setting is completed before setting the focus\n\n1.2.0 (2022-06-27)\n------------------\n- Update server to support Omni\n- Add move stage\n- Add get position\n- Add set flash duration\n- Add mandatory turning off of warranty\n- Check for connection loss and reconnect is closed\n- Check for sleeping device\n\n1.1.1 (2022-06-29)\n------------------\n- Update documentation\n\n1.1.0 (2021-12-03)\n------------------\n- Add change camera settings\n- Add set activate camera (brightfield, red-fluo, or green-fluo)\n- Change focus: \n make sure focus always happens in brightfield camera mode\n Add sleep after changing to focus so camera can move to new position\n- Update to new Cytosmart app\n\n1.0.4 (2021-04-15)\n------------------\n- Update Pillow\n- Fix installation requirements\n\n1.0.3 (2021-11-22)\n------------------\n- Update requirements of websocket and websocket-client to include version 1\n- Check if app is open before starting a new one\n\n1.0.2 (2021-04-15)\n------------------\n- Update pillow\n- Update license to ACADEMIC PUBLIC LICENSE\n\n1.0.1 (2021-01-14)\n------------------\n- Added support for LUX3 FL\n- Bugfix: toggle liveview when change zoom level\n\n1.0.0 (2020-09-15)\n------------------\n- Added multi lux support\n- Changed output from numpy array to pillow\n- Require serial number with function to get information\n- Add get_temperature\n\n0.1.2 (2020-06-30)\n------------------\n- Rename failing to pinging in print statement\n\n0.1.1 (2020-06-11)\n------------------\n- Update documentation\n- Make setup.py fit for PyPI\n \n0.1.0 (2020-05-20)\n------------------\n- Update lux server to latest version\n\n0.0.3 (2020-03-30)\n------------------\n- bugfix: files were not copied into package on linux\n\n0.0.2 (2020-03-24)\n------------------\n- Bugfix: stop waiting for response after sending a message\n\n0.0.1 (2020-03-16)\n------------------\n\n- Add function: Copy the luxconnector \n- Add function: focus change option\n- Add function: z-stack\n- Bugfix: add lux app to manifest\n\n0.0.0 (2020-03-13)\n------------------\n\nCopied basic package a start of luxconnector\n\n\n ACADEMIC PUBLIC LICENSE\n version 1.1\n\n Copyright (C) 2021\n\n\n Preamble\n\nThis license contains the terms and conditions of using AxionVueOpenAPI in\nnoncommercial settings: at academic institutions for teaching and research\nuse and for personal or educational purposes. You will find that this\nlicense provides noncommercial users of AxionVueOpenAPI with rights that are\nsimilar to the well-known GNU General Public License, yet it retains the\npossibility for AxionVueOpenAPI authors to financially support the development by\nselling commercial licenses. In fact, if you intend to use AxionVueOpenAPI in a\n\"for-profit\" environment, where research is conducted to develop or enhance\na product, is used in a commercial service offering, or when an entity uses\nAxionVueOpenAPI to participate in government-funded, EU-funded, military or similar\nresearch projects, then you need to obtain a commercial license.\nIn that case, or if you are unsure, please contact the Author imaging.support@axionbio.com\nto inquire about commercial licenses.\n\nWhat are the rights given to noncommercial users? Similarly to GPL, you\nhave the right to use the software, to distribute copies, to receive source\ncode, to change the software and distribute your modifications or the\nmodified software. Also similarly to the GPL, if you distribute verbatim or\nmodified copies of this software, they must be distributed under this\nlicense.\n\nBy modeling the GPL, this license guarantees that you're safe when using\nAxionVueOpenAPI in your work, for teaching or research. This license guarantees\nthat AxionVueOpenAPI will remain available free of charge for nonprofit use. You\ncan modify AxionVueOpenAPI to your purposes, and you can also share your modifications.\nEven in the unlikely case of the authors abandoning AxionVueOpenAPI entirely, this\nlicense permits anyone to continue developing it from the last release, and\nto create further releases under this license.\n\nWe believe that the combination of noncommercial open-source and commercial\nlicensing will be beneficial for the whole user community, because income from\ncommercial licenses will enable faster development and a higher level of\nsoftware quality, while further enjoying the informal, open communication\nand collaboration channels of open source development.\n\nThe precise terms and conditions for using, copying, distribution and\nmodification follow.\n\n ACADEMIC PUBLIC LICENSE\n\n TERMS AND CONDITIONS FOR USE, COPYING, DISTRIBUTION AND MODIFICATION\n\n0. Definitions\n\n\"Program\" means a copy of AxionVueOpenAPI, which is said to be distributed under\nthis Academic Public License.\n\n\"Work based on the Program\" means either the Program or any derivative work\nunder copyright law: that is to say, a work containing the Program or a\nportion of it, either verbatim or with modifications and/or translated into\nanother language. (Hereinafter, translation is included without limitation\nin the term \"modification\".)\n\n\"Using the Program\" means any act of creating executables that contain or\ndirectly use libraries that are part of the Program, running any of the\ntools that are part of the Program, or creating works based on the Program.\n\nEach licensee is addressed as \"you\".\n\n1. Permission is hereby granted to use the Program free of charge for\n noncommercial purposes, including teaching and academic research at\n universities, colleges and other educational institutions and personal\n non-profit purposes. 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