microdrop 2.0.post100.dev177009821

Microdrop is a graphical user interface for the DropBot Digital Microfluidics control system

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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](#no-existing-python-27-32-bit-windows-installation)
- [Existing `anaconda` (Python 2.7 32-bit Windows) installation](#existing-anaconda-python-27-32-bit-windows-installation)
- [Create a separate `conda` environment for MicroDrop 2.0](#create-a-separate-conda-environment-for-microdrop-20)
- [Other Python 2.7 32-bit Windows installation (using `pip`)](#other-python-27-32-bit-windows-installation-using-pip)
- [Configuration](#configuration)
- [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.

After installing, the directions in the [Configuration section](#configuration)
below can be used to:

- Create a MicroDrop user configuration
- Launch MicroDrop

### No existing Python 2.7 32-bit Windows installation ###

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 ###

Run:

conda install -c wheeler-microfluidics microdrop-2.0 microdrop-plugin-manager 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 2.0 ###

Run:

conda create -n microdrop-2.0 -c wheeler-microfluidics microdrop-2.0 microdrop-plugin-manager dmf-device-ui

To activate the MicroDrop 2.0 `conda` environment, run:

activate microdrop-2.0

To deactivate the MicroDrop 2.0 `conda` environment, run:

deactivate


### Other Python 2.7 32-bit Windows installation (using `pip`) ###

1. Update `pip`:

pip install -U pip

2. Install microdrop (find latest version number on [PyPi][3], e.g.,
`"microdrop>=2.0.post14.dev250849665"`):

pip install --find-links http://192.99.4.95/wheels --trusted-host 192.99.4.95 "microdrop>=2.0,<3.0"

**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*.


# Configuration #

To create a new MicroDrop settings directory with a batch file launcher, run
the following command using the Python installation used to install MicroDrop:

python -m microdrop.bin.create_portable_config <microdrop settings directory>

To launch MicroDrop, run:

<microdrop settings directory>\microdrop.bat


# 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:

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:

<microdrop settings directory>\microdrop.bat


[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/latest
[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

[install-plugins]: microdrop/static/images/plugins-install.gif


Credits
=======

Ryan Fobel <[e-mail]>

Christian Fobel <[e-mail]>