README

Date: 03/19/14
Authors: Evan Schwab (Megason Lab, Harvard Medical School)
Kishore Mosaliganti (Megason Lab, Harvard Medical School)



Installation
------------

First run ./install.sh to download the Bio-Formats command line tools and
loci_tools.jar file which will place these tools in a specified directory
called bioformatsTools/ within your working directory.


Usage
-----

ImageConversion.sh has one input parameter: the path-to-file to be converted
to megacapture format.

It must include the the appropriate .lsm or .zvi extension.
Creates folder	with same name as input file and same path with the .meg
metadata and the corresponding .png image files.

./ImageConversion.sh ../Data/SNAP-154443-0011.zvi

ThreadedImageConversion.sh has one input parameter: the path-to-file to be converted
to megacapture format. It is multithreaded and consequently runs faster.


How to add a new file format
----------------------------

As evidenced by .lsm and .zvi, most format files have different metadata field names.
Therefore, in order to add a new file format to ImageConversion.sh it must be added 
as another { elif [ "$EXTENSION" == "ext" ]; then } statement.  Then there are 13 
metadata fields that must be put in an array EXT.  These fields will be replaced by 
the MEG megacapture metadata fields in sed "s/${EXT[${i}]}:/${MEG[${i}]}/" input.tmp > ext.tmp.  
But first the EXT fields must be in the correct form.

Where I have written sed -e 's/\tSizeT =/SizeT:/g' -e 's/\tSizeZ =/SizeZ:/g' , etc.
I am changing the fields of various forms like \tFIELD = into FIELD: so that they can
be changed automatically in the sed "s/${EXT[${i}]}:/${MEG[${i}]}/" loop above.

So since each file format metadata is different these exceptional field forms must be
taken care of on a case by case basis in order to ready it for the 
sed "s/${EXT[${i}]}:/${MEG[${i}]}/" loop.