Merge pull request #2190 from AllenInstitute/feature/2190-nicify_readme

Reformat main readme file

README.md

@@ -6,77 +6,89 @@
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 [![GitHub contributors](https://img.shields.io/github/contributors/AllenInstitute/MIES?style=plastic)](https://github.com/AllenInstitute/MIES/graphs/contributors)
 
-MIES is a proven \[[1](https://www.science.org/stoken/author-tokens/ST-374/full),
+## Multichannel Igor Electrophysiology Suite
+
+The Multichannel Igor Electrophysiology Suite (MIES) is a proven sweep based data acquisition
+software package for [intracellular electrophysiology](https://en.wikipedia.org/wiki/Electrophysiology#Intracellular_recording) (patch clamp) \[[1](https://www.science.org/stoken/author-tokens/ST-374/full),
 [2](https://doi.org/10.1038/s41586-021-03813-8),
 [3](https://doi.org/10.1038/s41593-019-0417-0),
 [4](https://elifesciences.org/articles/37349),
 [5](https://doi.org/10.1038/s41586-021-03813-8),
-[6](https://doi.org/10.7554/eLife.65482)\] sweep based data acquisition
-software package for intracellular electrophysiology (patch clamp). It offers
-top of its class flexibility and robustness for stimulus generation, data
+[6](https://doi.org/10.7554/eLife.65482)\].
+It offers top of its class flexibility and robustness for stimulus generation, data
 acquisition, and analysis.
 
 ## Highlights
 
-- Acquire data on up to eight headstage on a single DAC.
-- Run up to five DACs in parallel.
-- Create arbitrarily complex stimulus sets with an easy to use GUI
-- Export all data, including all of its metadata, into the industry-standard NWBv2-format and read it back in
-- Run custom code during data acquisition for Automatic Experiment Control
-- Completely automate the experimental setup using JSON configuration files
-- Interact with MIES from other programming languages (Python, C++, Javascript, ...) using ZeroMQ.
-- Comprehensive experimental metadata acquisition and browsing tools
-- Use the integrated scripting language for convenient on-the-fly data evaluation.
-- Fully backward compatible with every earlier MIES version
+- Run up to five DACs in parallel for scalable data acquisition.
+- Acquire data on up to eight headstage on a single DAC to probe up to 56 connections at once.
+- Create arbitrarily complex stimulus sets with an intuitive GUI.
+- Export all data, including all of its metadata, into the industry-standard [NWBv2-format](https://doi.org/10.1101/523035) and read it back in
+- Run custom code during data acquisition for Automatic Experiment Control and real-time adaptability.
+- Automate experimental setup using configuration files for streamlined workflows.
+- Interact with MIES from other programming languages (Python, C++, Javascript, ...) through [ZeroMQ](https://zeromq.org/).
+- Track and manage your experiments with comprehensive metadata acquisition and browsing tools.
+- Leverage the integrated scripting language for flexible, on-the-fly electrophysiology data evaluation.
+- Ensure compatibility with every earlier version of MIES, protecting your previous work and workflows.
 
-![Slideshow showing the main graphical user interfaces of MIES in Igor Pro](Packages/Artwork/readme-teaser.gif)
+## Getting started
 
-## Supported Hardware
-- Digital to analog converters (DAC):
-    - National Instruments:
-      * [PCIe-6341](https://www.ni.com/de-de/support/model.pcie-6341.html)
-      * [PCIe-6343](https://www.ni.com/en-us/support/model.pcie-6343.html)
-      * [PXI-6259](https://www.ni.com/en-us/support/model.pxi-6259.html)
-      * [USB-6346](https://www.ni.com/de-de/support/model.usb-6346.html)
+- Download the [latest release](https://github.com/AllenInstitute/MIES/releases/tag/latest)
+- Windows: Run the installer
+- MacOSX (analysis only): [Manual installation](https://alleninstitute.github.io/MIES/installation.html#manual-installation)
+- View the [documentation](https://alleninstitute.github.io/MIES/user.html)
 
-      Other NI hardware models can be added on request. Please open an issue from within MIES,
-  `MIES Panels->Report an issue`, for that.
+### Brief visual overview
 
-   - Instrutech/HEKA ITC:
-     * [16](http://www.heka.com/downloads/hardware/manual/itc16.pdf)
-      * [18](http://www.heka.com/downloads/hardware/manual/m_itc18.pdf)
-     * [1600](http://www.heka.com/downloads/hardware/manual/m_itc1600.pdf)
+![Slideshow showing the main graphical user interfaces of MIES in Igor Pro](Packages/Artwork/readme-teaser.gif)
 
-     ITC devices are at the End-Of-Service-Life (EOSL). National Instruments DACs are recommended for MIES users looking
-for new hardware.
+### Postsynaptic data analysis
 
-- Amplifier: Molecular Devices [700B](https://www.moleculardevices.com/products/axon-patch-clamp-system/amplifiers/axon-instruments-patch-clamp-amplifiers)
-- Pressure control (optional): ITC 18/1600 or National Instruments [USB 6001](https://www.ni.com/en-us/support/model.usb-6001.html)
+[![Demonstration of postsynaptic data analysis](https://img.youtube.com/vi/O2WxPzBsEfc/0.jpg)](https://www.youtube.com/watch?v=O2WxPzBsEfc)
+
+Video tutorial of the postsynaptic potential/postsynaptic current data (PSX) analysis module
 
 ## Required Software
 
 - [Igor Pro 9 (nightly) or later](https://alleninstitute.github.io/MIES/installation.html#igor-pro-update-nightly)
 
-### Acquisition
+### For Data Analysis
 
-- Windows 10 x64
+- Windows 10 64-bit or MacOSX 10.10
+
+### For Data Acquisition
+
+- Windows 10 64-bit
 - [NIDAQ MX XOP](https://www.wavemetrics.com/products/nidaqtools/nidaqtools.htm)
 
-### Data evaluation
+## Supported Hardware
 
-- Windows 10x64 or MacOSX 10.10
+- Digital to analog converters (DAC):
+  - National Instruments:
+    - [PCIe-6341](https://www.ni.com/de-de/support/model.pcie-6341.html)
+    - [PCIe-6343](https://www.ni.com/en-us/support/model.pcie-6343.html)
+    - [PXI-6259](https://www.ni.com/en-us/support/model.pxi-6259.html)
+    - [USB-6346](https://www.ni.com/de-de/support/model.usb-6346.html)
 
-## Getting started
+      Other NI hardware models can be added on request. Please open an issue from within MIES,
+  `MIES Panels->Report an issue`, for that.
 
-- [Download](https://github.com/AllenInstitute/MIES/releases/tag/latest) the latest release
-- Windows: Run the installer
-- MacOSX (Analysis only): [Manual installation](https://alleninstitute.github.io/MIES/installation.html#manual-installation)
-- [View](https://alleninstitute.github.io/MIES/user.html) the documentation
+  - Instrutech/HEKA ITC:
+    - [16](http://www.heka.com/downloads/hardware/manual/itc16.pdf)
+    - [18](http://www.heka.com/downloads/hardware/manual/m_itc18.pdf)
+    - [1600](http://www.heka.com/downloads/hardware/manual/m_itc1600.pdf)
+
+     ITC devices are at the End-Of-Service-Life (EOSL). National Instruments DACs are recommended for MIES users looking for new hardware.
+
+- Amplifier: Molecular Devices [700B](https://www.moleculardevices.com/products/axon-patch-clamp-system/amplifiers/axon-instruments-patch-clamp-amplifiers)
+- Pressure control (optional):
+  - [QPV High Resolution Pressure Regulator](https://proportionair.com/product/qpv/) from Proportion-Air, Inc.; Part name: QPV regulator (custom, see part No), -10 psi to +10 psi; Part no.: QPV1TBNEEN10P10PSGAXLDD
+  - controlled through ITC 18/1600 or National Instruments [USB 6001](https://www.ni.com/en-us/support/model.usb-6001.html)
 
 ## Support statement
 
 The last released version receives fixes for all critical bugs.
 
 ## Bug reporting
 
-[Instructions](https://alleninstitute.github.io/MIES/reportingbugs.html)
+[Report a Bug](https://alleninstitute.github.io/MIES/reportingbugs.html)