From 17033e81306eaba0e51b1bbd664af827c6b98f1d Mon Sep 17 00:00:00 2001 From: Talon Chandler Date: Mon, 17 Apr 2023 17:59:57 -0700 Subject: [PATCH] Minor documentation updates for 0.3.0 (#344) * typo * don't mention CLI in README * remove apple silicon-specific instructions * Add link to microscope installation guide to main README --- README.md | 12 +++--------- docs/development-guide.md | 10 ---------- docs/microscope-installation-guide.md | 2 +- 3 files changed, 4 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 9e05fa8d..010af001 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ The acquisition, calibration, background correction, reconstruction, and applica Syuan-Ming Guo, Li-Hao Yeh, Jenny Folkesson, Ivan E Ivanov, Anitha P Krishnan, Matthew G Keefe, Ezzat Hashemi, David Shin, Bryant B Chhun, Nathan H Cho, Manuel D Leonetti, May H Han, Tomasz J Nowakowski, Shalin B Mehta, "Revealing architectural order with quantitative label-free imaging and deep learning," eLife 2020;9:e55502 DOI: 10.7554/eLife.55502 (2020). ``` -`recOrder` is to be used alongside a conventional widefield microscope fitted with a universal polarizer (Panel A below). The universal polarizer allows for the collection of label-free information including the intrinsic anisotropy of the sample and its relative phase (density). These measurements are collected by acquiring data under calibrated, polarization-diverse illumination followed by a computational reconstruction. The overall structure of `recOrder` is shown in Panel B, highlighting the two different usage modes and their features: graphical user interface (GUI) through a napari plugin, and a command line interface (CLI). +`recOrder` is to be used alongside a conventional widefield microscope fitted with a universal polarizer (Panel A below). The universal polarizer allows for the collection of label-free information including the intrinsic anisotropy of the sample and its relative phase (density). These measurements are collected by acquiring data under calibrated, polarization-diverse illumination followed by a computational reconstruction. The overall structure of `recOrder` is shown in Panel B, highlighting the structure of the graphical user interface (GUI) through a napari plugin. ![Flow Chart](https://github.com/mehta-lab/recOrder/blob/main/docs/images/recOrder_Fig1_Overview.png?raw=true) @@ -34,13 +34,6 @@ conda create -y -n recOrder python=3.9 conda activate recOrder ``` -> *Apple Silicon users please use*: -> -> ```sh -> CONDA_SUBDIR=osx-64 conda create -y -n recOrder python=3.9 -> conda activate recOrder -> ``` - Install `recOrder-napari`: ```sh @@ -53,4 +46,5 @@ Open `napari` with `recOrder-napari`: napari -w recOrder-napari ``` -For more help, see [`recOrder`'s documentation](./docs). +For more help, see [`recOrder`'s documentation](./docs). To install `recOrder` +on a microscope, see the [microscope installation guide](./docs/microscope-installation-guide.md). diff --git a/docs/development-guide.md b/docs/development-guide.md index 770e7038..18c26fd3 100644 --- a/docs/development-guide.md +++ b/docs/development-guide.md @@ -9,16 +9,6 @@ conda activate recOrder ``` - > *Apple Silicon users please use*: - > - > ```sh - > CONDA_SUBDIR=osx-64 conda create -y -n recOrder python=3.9 - > conda activate recOrder - > ``` - > - > Reason: `napari` requires `PyQt5` which is not available for `arm64` from PyPI wheels. - > Specifying `CONDA_SUBDIR=osx-64` will install an `x86_64` version of `python` which has `PyQt5` wheels available. - 2. Clone the `recOrder` directory: ```sh diff --git a/docs/microscope-installation-guide.md b/docs/microscope-installation-guide.md index c5b07e7c..d54a00de 100644 --- a/docs/microscope-installation-guide.md +++ b/docs/microscope-installation-guide.md @@ -72,4 +72,4 @@ Finally, enable port access so that `Micromanager` can communicate with recOrder From the `recOrder` window, click `Switch to Online`. If you see `Success`, your installation is complete and you can [proceed to the napari plugin guide](./napari-plugin-guide.md). -If you you see `Failed`, check that `Micromanager` is open, check that you've enabled `Run server on port 4827`. If the connection continues to fail, report an issue with you stack trace for support. +If you you see `Failed`, check that `Micromanager` is open, check that you've enabled `Run server on port 4827`. If the connection continues to fail, report an issue with your stack trace for support.