JSpot DNA micro-array software

Installation Instructions

Pre-requisites

JSpot is written in Java and requires that a Java runtime is installed. Currently I recommend using version 1.3. It also needs the Advanced Imaging toolkit. So, do the following:

  1. Download and install the JRE or SDK 1.3 from Sun's website
  2. Download and install the Advanced Imaging JRE or SDK 1.3 from here

[Note: the JRE is the minimum download, the SDK is for developers]

IMPORTANT: Check that Java is installed correctly by typing java -version at a command prompt.

Installing JSpot

Select a version to download (right click the link and select 'Save as...'):

This software is still BETA software and should be used for testing only.

VersionUpdatedDownloadSizeNotes
JSpot v0.3-E 10th Nov 2002 JSpot0_3.jar 2.3M Two-pass variational spot finding, multi-channel images, resumable processing
JSpot v0.2-G 8th May 2002 JSpot0_2.jar 411.1K Added learning of background intensity model
JSpot v0.1-E 9th April 2002 JSpot0_1.jar 367K First release

Put the downloaded file JSpot0_X.jar in a directory called JSpot.

Running JSpot v0.1 (use similar process for more recent versions)

Check JSpot is installed correctly:

  1. Change to the JSpot directory.
  2. Type:

    java -jar JSpot0_1.jar

  3. You should get a short description of how to use JSpot, such as:
    4. Spot v0.1-D, (c) 2002 John Winn, University of Cambridge
Usage:
  JSpot -image imageFile -layout layoutFile [-output outputFile]
        -view (on | raw | off)] [-test]
where:
  imageFile: slide image to process
  layoutFile: the file containing slide layout. Currently only
              MWBR files are supported.
  outputFile: the output XML filename (this will be derived
              from the image name if not specified)
  view: on = shows progress on equalised image
        raw= shows progress on raw image
        off= doesn't show progress
You can then run JSpot on an image file, such as

java -jar JSpot0_1.jar -image MyArrayImage.tif -layout MyLayout.mwbr

As JSpot can take tens of minutes to analyse an image, you can test your setup using the -test switch which just analyses the first subgrid, for example:

java -jar JSpot0_1.jar -image MyArrayImage.tif -layout MyLayout.mwbr -test

Notes: