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caMicroscope 2.0, is built using a number of great open source tools to help visualize massive digital microscopy images. These include IIPServer to serve images, IIPServer compatible webclients (IIPMooviewer or OpenSeaDragon) and a set of libraries to help convert images into formats that IIPServer can render. I was never able to find a single place where this information had been aggregated, so I decided to put one together. These are rather comprehensive set of instructions that include:

  1. Build & install IIPServer on a CentOS machine.
  2. Install and Configure two awesome clients — IIPMooviewer and OpenSeaDragon
  3. Support large images using BigTIFF and Vips
  4. Support large microscopy images using OpenSlide and Vips (Optional: only if you care about digital microscopy)

Step 1.1 Configure the Centos Machine

Prepare a Centos 6 machine
Add yourself to sudo (How?)
Update

export PATH = $PATH

Update
Update

 

export PATH = $PATH

 

Update

Step 1.2. Install BigTiff

Why: BigTiff allows you to work with tiff files that are greater than 4GB in size

Downloadhttp://www.remotesensing.org/libtiff/  Version: 4.0.3

Prepare a Centos 6 machine
Add yourself to sudo (How?)
Update

export PATH = $PATH

Update
Update

 

export PATH = $PATH

 

Update

Step 1.2. Install BigTiff

Why: BigTiff allows you to work with tiff files that are greater than 4GB in size

Downloadhttp://www.remotesensing.org/libtiff/  Version: 4.0.3

1. Install BigTIFF (v. 4.0.3)


Download from http://www.remotesensing.org/libtiff/

Next, we make sure this library is loaded and accessible to all

Create a new file called libtiff.4.0.3.cfg file /etc/ld.so.conf.d

insert one line in that file that has the name of the <Install Directory>/lib

run ldconfig

2. Install Openslide (v. 3.3.2)


Download source from http://openslide.org/download/

Next, we make sure this library is loaded and accessible to all

Create a new file called libtiff.4.0.3.cfg file /etc/ld.so.conf.d

insert one line in that file that has the name of the <Install Directory>/lib

run ldconfig