microdrop 2.0.post115.dev9233482

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MicroDrop is a graphical user interface for the [DropBot][1] digital
microfluidics control system (described in detail in [Fobel et al., Appl. Phys.
Lett. 102, 193513 (2013)][2]).

If you use this information in work that you publish, please cite as
appropriate.

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**Table of Contents** *generated with [DocToc](https://github.com/thlorenz/doctoc)*

- [Installation](#installation)
- [No existing Python 2.7 32-bit Windows installation **(recommended)**](#no-existing-python-27-32-bit-windows-installation-recommended)
- [Existing `anaconda` (Python 2.7 32-bit Windows) installation **(recommended)**](#existing-anaconda-python-27-32-bit-windows-installation-recommended)
- [Create a separate `conda` environment for MicroDrop](#create-a-separate-conda-environment-for-microdrop)
- [Other Python 2.7 32-bit Windows installation (using `pip`, **not recommended**)](#other-python-27-32-bit-windows-installation-using-pip-not-recommended)
- [**Shortcuts**](#shortcuts)
- [**Import** profile](#import-profile)
- [Profile Manager **(new)**](#profile-manager-new)
- [Import profile](#import-profile)
- [Remove profile](#remove-profile)
- [Install plugins](#install-plugins)
- [Featured plugins](#featured-plugins)
- [Install plugins through MicroDrop plugin manager (`mpm`)](#install-plugins-through-microdrop-plugin-manager-mpm)
- [Install plugins through MicroDrop GUI](#install-plugins-through-microdrop-gui)
- [Credits](#credits)

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# Installation #

MicroDrop can be installed using any of the methods below.

### No existing Python 2.7 32-bit Windows installation **(recommended)** ###

Download installer for latest [MicroDrop 2.0 release][4].

This installer is a customized distribution of the popular [`Miniconda`][5]
Python.


### Existing `anaconda` (Python 2.7 32-bit Windows) installation **(recommended)** ###

Run:

conda install -c wheeler-microfluidics "microdrop>=2.0,<3.0" microdrop-launcher dmf-device-ui

**Note** *the `-c wheeler-microfluidics` flag allows installing conda packages
from the `wheeler-microfluidics` channel*.


### Create a separate `conda` environment for MicroDrop ###

Run:

conda create -n microdrop -c wheeler-microfluidics "microdrop>=2.0,<3.0" microdrop-launcher dmf-device-ui

To activate the MicroDrop `conda` environment, run:

activate microdrop

To deactivate the MicroDrop `conda` environment, run:

deactivate

See ["Managing environments"][15] section of Conda documentation for more
information.


### Other Python 2.7 32-bit Windows installation (using `pip`, **not recommended**) ###

1. Update `pip`:

pip install -U pip

2. Install microdrop (find latest version number on [PyPi][3], e.g.,
`"2.0.post110.dev156674653"`):

pip install --find-links http://192.99.4.95/wheels --trusted-host 192.99.4.95 <microdrop version> microdrop-launcher dmf-device-ui

**Note** *`192.99.4.95` is the IP address of the official MicroDrop update
server where MicroDrop dependencies not available on PyPI are stored as
wheels*.

<img align="right" src="microdrop/static/images/microdrop-shortcuts.png" />

## **Shortcuts** ##

If MicroDrop is installed using a Conda Python distribution (including the [official installer][1])

- **Documentation**: Open [online MicroDrop documentation][readthedocs].
- **GitHub project**: Open MicroDrop [GitHub project page][github].
- **MicroDrop Profile Manager**: Launch MicroDrop profile manager.
- **MicroDrop environment prompt**: Launch Windows command prompt with
MicroDrop Conda environment activated.
- **MicroDrop**: Launch MicroDrop if only one **profile** is available
*(default)*. Otherwise, launch **MicroDrop Profile Manager** to select
**profile** to launch.
* **Tip**: Right-click on shortcut to **pin** to **taskbar** for easy
access.

## **Import** profile ##

If existing **profile** directory is not automatically found, it can be
manually **imported** by launching the **"MicroDrop Profile Manager"**
shortcut.

See [Profile Manager](#profile-manager-new) section below.

# Profile Manager **(new)** #

In environments where, for example, multiple users are using the same computer
to perform MicroDrop experiments, it can be helpful to create separate
MicroDrop **profiles**. Each MicroDrop **profile** contains **devices** and
**plugins**, as well as **experiment logs**.

The **MicroDrop Profile Manager** provides an interface to manage one or more
MicroDrop profiles. Initially, the **default profile path** (i.e.,
`<Documents>\Microdrop`) is listed.

As shown below:

- Profiles are **listed** according when they were last launched, with the
**most recently used profile first**.
- Existing profiles may be **imported**.
- Listed profiles may be **removed** from the profile list (and optionally
**deleted** entirely).
- Listed profiles may be **opened** in the system file browser.
- MicroDrop may be **launched** using any of the listed profiles.

![MicroDrop Profile Manager][microdrop-profile-manager]


## Import profile ##

When an existing **profile** is imported, **plugin** dependencies are installed
while the following dialog is displayed:

![MicroDrop Profile Manager - install dependencies][install-dependencies]

## Remove profile ##

The following **dialog** is displayed when the **Remove** button for a listed
profile is **clicked**:

![MicroDrop Profile Manager - remove profile][remove-profile]

Clicking the **Remove** button in the dialog removes the corresponding
**profile** from the list, but **does not** delete any files. The **profile**
can be imported to add it back to the profile list.

**Warning:** Clicking the **Remove with data** button in the dialog removes the
corresponding **profile** from the list, **and deletes the profile directory**.
This **cannot be undone**.


# Install plugins #

Plugins can either be installed using the [MicroDrop plugin
manager](#install-plugins-through-microdrop-plugin-manager-mpm) command-line
tool, or through the [MicroDrop user
interface](#install-plugins-through-microdrop-gui).

### Featured plugins ###

- [`device_quality_control_plugin`][6]:
* Perform impedance scan across all channels on microfluidics chip.
* Can be used to identify suspected broken electrode traces.
* **Requires `dmf_control_board_plugin`**.
- [`dmf_control_board_plugin`][7]
* Control actuation parameters for the [DropBot][12] open-source Digital
Microfluidic (DMF) automation system.
- [`dmf_device_ui_plugin`][8]
* Displays interactive DMF chip geometry.
* Optional augmented reality interface, where device drawing is overlaid
on live webcam video feed.
- [**`droplet_planning_plugin`**][13]
* Click and drag mouse over series of electrodes to create a route.
* Hold <kbd>Alt</kbd>, click on source electrode, and drag to target
electrode to automatically route between electrodes.
* Finish route at starting point to form a cycle that may be repeated
(i.e., mixing) either:
- A set number of repetitions
- A time duration
- [`step_label_plugin`][10]
* Optionally add text label to any step in protocol.
* Most recent and next upcoming labelled steps are indicated while running
protocol.
- [`user_prompt_plugin`][11]
* Add (optional) user prompt for each step in protocol (e.g., "Confirm
sample is loaded.")
* Protocol execution is paused until user confirms **OK** to proceed.
* If user selects `Cancel`, protocol is stopped.

### Install plugins through MicroDrop plugin manager (`mpm`) ###

The Microdrop plugin manager is a command-line tool (inspired by `pip`) for
managing (e.g., install, uninstall) Microdrop plugins.

For full usage details, see the [project home page][14].

Basic usage to install a plugin:

- Start MicroDrop environment command prompt using the following shortcut:

![][microdrop-environment-shortcut]

- In MicroDrop environment command prompt, run:

python -m mpm -c <microdrop settings directory>\microdrop.ini install plugin [plugin [plugin ...]]

To install featured plugins:

python -m mpm -c <microdrop settings directory>\microdrop.ini install dmf_control_board_plugin dmf_device_ui_plugin droplet_planning_plugin user_prompt_plugin step_label_plugin

### Install plugins through MicroDrop GUI ###

1. Install plugins:

![Install MicroDrop plugins][install-plugins]

2. Relaunch MicroDrop.


[1]: http://microfluidics.utoronto.ca/microdrop
[2]: http://dx.doi.org/10.1063/1.4807118
[3]: https://pypi.python.org/pypi/microdrop
[4]: https://github.com/wheeler-microfluidics/microdrop/releases
[5]: http://conda.pydata.org/miniconda.html
[6]: https://github.com/wheeler-microfluidics/device-quality-control-plugin
[7]: https://github.com/wheeler-microfluidics/dmf_control_board_plugin
[8]: https://github.com/wheeler-microfluidics/dmf_device_ui_plugin
[9]: https://github.com/wheeler-microfluidics/metadata_plugin
[10]: https://github.com/wheeler-microfluidics/step_label_plugin
[11]: https://github.com/wheeler-microfluidics/user_prompt_plugin
[12]: http://microfluidics.utoronto.ca/dropbot/
[13]: https://github.com/wheeler-microfluidics/droplet-planning-plugin
[14]: https://github.com/wheeler-microfluidics/mpm
[15]: http://conda.pydata.org/docs/using/envs.html

[github]: https://github.com/wheeler-microfluidics/microdrop/tree/release-1.0
[readthedocs]: http://microdrop.readthedocs.io/
[install-plugins]: microdrop/static/images/plugins-install.gif
[microdrop-environment-shortcut]: microdrop/static/images/microdrop-environment-shortcut.png
[microdrop-profile-manager]: microdrop/static/images/microdrop-plugin-manager-annotated.png
[install-dependencies]: microdrop/static/images/plugin-manager-install-dependencies.png
[remove-profile]: microdrop/static/images/plugin-manager-remove.png

Credits
=======

Ryan Fobel <ryan@fobel.net>

Christian Fobel <christian@fobel.net>