Installing the software
Next: Basic Concepts and Terms Previous: Introduction

SectionView and MAPaint are two views of the same program. When started in sectionView mode the number of options is reduced and no editing of domains is possible.  In terms of navigating through the 3D volume the programs are the same.

MAPaint is currently only compiled for unix machines. To use the program from the command line e.g. as in an X-terminal do installation steps 1, 2 and 4 below. To use it from your browser do installation steps 1, 2 and 3.
 

Step1: copy the programs to your hard disk

Whilst it is possible to leave the program binaries on the CD-ROM it is much more convenient to copy them to a directory that is on your computer hard disk and set your search path to include that location. You may need root permissions on your machine for this purpose. Assuming you have the required permission to create directories and files on your machine do the following:
  1. Choose a pathname for the installed files <INSTALL BIN DIR> - e.g. /opt/MouseAtlas/bin
  2. Create a directory with that path e.g. -
  3. Put the CD in the CD-ROM drive and find its path <CD-ROM path> e.g. under Solaris it will probably be /cdrom/cdrom0
  4. Choose the required machine type <MACH> from:
  5. Copy the binaries with the command: "cp <CD-ROM path>/macd/bin/<MACH>/*  <INSTALL BIN DIR>" e.g.
  6. Check the permissions of the installed binaries:
  7. If you want to use the software on other unix machines, make sure the install directory is shared or repeat the process for each machine.

Step 2: Set your binaries search path to find the program

To run the program you need to set the search path that the unix shell uses to locate programs. You will need to edit the shell resource file which is in your home directory:
  1. Find out which shell you use e.g. sh, ksh, csh etc (if need be ask your administrator)
  2. If it is Bourne shell flavour (sh, ksh, bash) edit the file .profile in your home directory and put in two lines at the end (note substitute the <INSTALL BIN DIR> you selected for /opt/MouseAtlas/bin):
  3. If it is C shell flavour csh or tcsh then edit the file .cshrc or .tcshrc in your home directory respectively and put in the two lines (note substitute the <INSTALL BIN DIR> you selected for /opt/MouseAtlas/bin):
  4. Execute the new startup files, or re-login to make sure you get the new path, if you want to start the programs from the html browser then you will need to restart it:

Step 3: Set your html browser to use MAPaint for Woolz files

Somewhere in your html browser there will be the option to set an "application" to be associated with particular "MIME" types or file types. These are determined by the file extension and to make the CD-ROM links for sectionView usable you need to set the application associated with the Woolz data type (extensions .wlz, .Wlz) to be MAPaint. How to set it depends on your browser.

Netscape 4.5+:

From the "Edit" menu select "Preferences..." and within the dialog that appears select "Navigator->Applications" as shown by the yellow bar in the image below:


 

Press the "New" button to get the dialog:


 

Define the new type as shown where /cdrom/cdrom0/reconstructions is the location of the CD directory on your machine followed by "reconstructions". For example under Solaris the default directory is /cdrom/cdrom0 therefore we type in as shown. This may be different on other machines. Note the full application startup line is:

MAPaint -cdrom /cdrom/cdrom0/macd/reconstructions %s

Internet Explorer 4+ on unix:

Essentially the same as for Netscape but now the  applications are set from "View->Internet Options..." button to give the dialog below and select the "Mapping" tab:

Click the "New Association" button and fill in the dialog as follows:

where the full Command Line is: "MAPaint -cdrom/cdrom0/macd/reconstructions %1"

Press "Apply Association"  to give:

and then "OK".

Your browser should now start the application correctly. Test it by clicking here, if all is well you should get sectionView starting up with no default reference image and with a "File->Theiler Stage" menu which includes "ts14". On selecting this option the Theiler Stage 14 embryo and anatomy will be loaded.

Step 4: Starting MAPaint from the command line


Put the CD-ROM in and from and X-terminal or other command line interface, for SectionView type:
 

and for MAPaint type: then select the required TheilerStage. Note substitute your cdrom directory if it is different to /cdrom/cdrom0.
 
 

Next: Basic Concepts and Terms Previous: Introduction

Richard Baldock
11th July 1998