From d50f0df92732b6fc24935df064ab416be4eb9c0c Mon Sep 17 00:00:00 2001 From: ackman678 Date: Mon, 2 Jun 2014 08:58:45 -0400 Subject: [PATCH] Updated install instructions * to reflect the switch to bfmatlab toolbox from the deprecated loci_tools.jar --- README.md | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 88dfb45..45878c3 100644 --- a/README.md +++ b/README.md @@ -20,9 +20,7 @@ There are also a number of miscellaneous functions for data analysis, fetching o ## Core dependencies ## * matlab with the signal processing and image processing toolboxes -* `loci_tools.jar` a java plugin for opening many different microscopy image/tiff file formats - * included, but up-to-date version can be found at [ome website](http://www.loci.wisc.edu/ome/ome-tiff.html) or through the ImageJ plugins page. - * should be placed in the `CalciumDX/` folder +* [bfmatlab](http://www.openmicroscopy.org/site/support/bio-formats5/users/matlab/index.html), a matlab toolbox containing the bio-formats java plugin and a `bfopen.m` reader function for opening many different microscopy image/tiff file formats. ## Non-core dependencies ## Several functions (mostly non-core gui) depend on the following freely available toolboxes: @@ -34,12 +32,9 @@ Several functions (mostly non-core gui) depend on the following freely available # Installation # 1. Clone CalciumDX from GitHub into your *MATLAB* user folder. -2. Add CalciumDX/CalciumDX to your [matlab path][matlabSearchPath] -3. Add CalciumDX/CalciumDXevents to your matlab path -4. *Optional:* Install the non-core dependency toolboxes - * download from the respective sites listed above - * move the toolboxes into your matlab user home folder - * add their folders and subfolders to your matlab path. +2. Add CalciumDX and subfolders to your [matlab path][matlabSearchPath] +3. Install the core dependency toolboxes (bfmatlab). Add them your matlab search path or use the `addpath(genpath('$PATH/$MATLABHOME/toolbox'))` syntax at the command prompt when starting up matlab with each toolbox. +4. *Optional:* Install the non-core dependency toolboxes. Same as above, add their folders and subfolders to your matlab path. ## Updates ##