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cellbaseTransferTool

Transfer software documentation

About the software

The 'Transfer' software was developed for image copy, move and conversion. The current supported formats are ScanR, Zeiss LSM and OME.TIF. This document explains how to use it and how to extend it.

It was developed by Ruben Gomez.

Using transfer software

The transfer software works under Windows XP and starts by double clicking the application file 'transfer.hta'. Once this is done, the interface opens and displays all the options.

  • Choose source: Users should select a folder containing their experiment.
  • Choose target: Users should select a folder to transfer their experiment.
  • 'Copy to target': Do a transfer duplicating the data in the target folder.
  • 'Move to target': Do a transfer moving the data to the target folder.
  • 'Compress': It's optional but necessary to save disk space.
  • 'Uncompress': It's optional but necessary to open the images faster.
  • 'Convert to OME.TIF': The load in cellBASE is only possible if the data has been previously converted to OME.TIF. Proprietary formats are NOT supported.
  • 'Rename channels to numbers': The load in cellBASE is only possible if the data has been previously converted to OME.TIF and the channels are numbers.
  • 'Online conversions': In some circustamces the user may want to run a conversion during the microscope run. That only works when the plate is acquired completely and there are no wells disabled.
  • 'Use a microscope-in file to label': The selected file will be used to label the images resulting from converting the files. The microscope-in files have 6 columns separated by '--'.

Requirements

The tool only runs on Windows XP and is completely contained in the folder Transfer. The bio-formats library, the libtiff binaries for windows and some dlls and tools are included with the software.

Location of the required software

The software and all it's dependencies are located under the network location almfscreen\almfscreen\cellbase\transfer

Extending the transfer software

Main program

The 'Transfer' software itself uses HTA technology (HTML Application) that consists in HTML code and VBScript. The code is located in the file 'transfer.hta'. In order to edit the code any text editor is necessary. VBScript is an scripting language derived from Visual Basic and has all of it's instructions and basic functions

The bio-formats library

The bio-formats library is also included in the package, as it is explained in the documentation file Integrating Bioformats with cellBASE. The files 'loci_tools.jar' and 'loci_tools_online.jar' are compiled modifications of the original code.

Important considerations

In order to implement all the desired functionality, 1 out of 3 different tools is automatically selected by the 'Transfer' tool. The 3 tools are 'robocopy.exe', 'tiffcp' and (bioformats) ImageConverter. When any of these tools requires parameters to run, the parameters are displayed on the graphical interface. One should observe these options while debugging the tool to extend it.