~~NOTOC~~
====== File Converter - Perkin Elmer Tiff Series to 3D stacks ======

==== Author ====

Kota Miura\\
Centre for Molecular and Cellular Imaging (CMCI)\\
EMBL Heidelberg\\ 
miura at embl dot de Tel: +49 6221 387 404 \\

==== History ====

2007/6/5: 1st version\\ \\ 
==== Source ====

Released under the GNU General Public License. 
==== Requires ====
 
ImageJ ver 1.37j or higher ([[http://rsb.info.nih.gov/ij/upgrade/|ImageJ, upgrade page]]). 
==== Installation ====

Download [[http://cmci.embl.de/dls/K_convert2MPT3D.ijm|K_convert2MPT3D.ijm]] to a place where you can access easily. Install the macro by [Plugins->Macros->Install...].

 ==== Description ====

Converts xyzt time series (single tiff series) generated by[[http://www.embl-heidelberg.de/almf/html/PE_Plugins.htm|Perkin-Elmer Loader (E. Seitz, ALMF)]] to 3D stack time series (multiple 3D stacks) for 3D tracking using "[[http://rsb.info.nih.gov/ij/plugins/track/track.html|Manual Tracking]]" plugin.\\ \\ Perkin-Elmer Loader ([[http://www.embl-heidelberg.de/almf/html/PE_Plugins.htm|Link]]) converts files generated by UltraviewRS and ERS RAW to a tiff-file series. These tiff files are named as follows:\\ \\ ? 
    Z000_c1_T0000.tif ? 
    Z000_c1_T0001.tif 
    ... ? 
    Z%%***_%%c1_T%%****%%.tif 
The macro produces?Z-stack for each time points (metamorph format). For example, if there were 30 Z slices and 100 time points, original tiff-series would have 3000 single XY files. This macro converts these 3000 files to 100 tiff-stacks, each containing 30 z-frames. \\ 
In addition, the macro generates a stack named "projection2D.tif" containing maximum intensity projection of each time points. In the example above,?projection2D.tif stack would have 100 frames. Each frame in this projection stack is added with the file name of original 3D stack as metadata (slice label). This metadata is used in the [[http://rsb.info.nih.gov/ij/plugins/track/track.html|Manual Tracking plugin]] when it retrieves Z coordinates from 3D stacks.\\ \\ 
==== Work Flow ====

**1.?** After installation, Do **[Plugins -> Macros -> Set Path]**. In the first dialog, choose a folder where the source tiff files are contained. In the second dialog, choose a folder where the converted files will be saved. This operation stores path to these folders in memory.\\ \\ 
**2.** Do **[Plugins -> Macros -> do Processing]**. In the first dialog window, input the number of z-slices. In the second dialog, input the number of time points. Be Careful: since the frame number start from 0, the last frame number + 1 is the total number of frames in z or t. For example,? if the last time point is "36", then there are 37 time points. \\ \\ 
3. In [[http://rsb.info.nih.gov/ij/plugins/track/track.html|Manual Tracking Plugin]]: Use the "Projection2D.tif" for the tracking in xy plane. \\ \\
4. In [[http://rsb.info.nih.gov/ij/plugins/track/track.html|Manual Tracking Plugin]]: Click "Retrieve Z coordinates" . Then in dialog, choose the destination folder (where files will be saved. You set this in 1) . \\ \\ 
\\ \\ 
**Acknowledgement:**\\ \\ Thanks to Fabrice Cordelieres@ Insititute Curie for telling me about the details on how manual tracker reads 3D files.\\