Batch Export Macro for AIM and

ZEN Batch export is a free macro available for AIM and ZEN that enables the user to export and convert multiple .lsm files into other file types, such as .bmp, .jpg, .gif, .tif, .avi, and .mov. Any questions or concerns can be directed to the ZEISS Product and Applications Support group at 1-800-509-3905 or Support@zeiss.com

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Installation of the Batch Export macro There are different versions of the Batch Export macro for AIM and ZEN. For AIM, the batch export macro can be found in this folder: C:\AIM\Macros\AdvancedTimeSeries\FileExport\FileExport.lvb Or in this folder: C:\AIM\Macros\FileExport.lvb ** The name of the .lvb file may be slightly different for different versions of AIM. Essentially, you should look for a .lvb file with the name “File Export” along with other numbers, example: “FileExportv28.lvb.” For ZEN, the batch export macro can be found in this folder: C:\ZEN\Macros\FileExportZEN.lvb If the macro is missing, it can be downloaded off of the ZEISS FTP site. To access the FTP site, use Internet Explorer to go to: ftp://lsm.zeiss.com/ Then open the site in Windows Explorer by clicking on "Page" and then "Open FTP Site in Windows Explorer". This is illustrated in Figure 1.

Figure 1: How to open the FTP site in Windows Explorer

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When prompted use "lsmusa" for the log-in and "tfc" for the password (no quotations). Then navigate to: /LSM/User_Area/Software/ As the Batch Export macro is modified for each software version, the next folder selection will be if the user has AIM or ZEN. For AIM, select “LSM5_Macros” and then the appropriate software version. Then continue to /FreeMacros. For AIM versions 3.2 and older, there will be a .exe file with the name “File Export” and a version number. Download this to the desktop and doubleclick to install. This will install to C:\AIM\Macros\AdvancedTimeSeries\FileExport\FileExport.lvb For AIM versions 3.5 and newer, you will need to go into /FreeMacros/FileExport. There will be a .lvb file that can be copied and pasted to the appropriate folder (C:\AIM\Macros). For ZEN, go to /ZEN_Macros/(select ZEN version)/FreeMacros/. Copy and paste FileExportZEN.lvb to C:\ZEN\Macros. After the macro has been downloaded off of the FTP site, it must be installed into AIM or ZEN software. For AIM, click on “Macro” to reveal the Macro sub-menu (Figure 2, Step 1). You will need to assign the macro to an empty button. Empty buttons are labeled as “n.n” (Figure 2). These buttons are numbered from left to right, top and then bottom. In the example in Figure 2, “EventPoll” is assigned to button number 1, FRET+ is assigned to button number 6, and Optimize Live is assigned to button number 9. You can also choose to assign the macro to a button that is already in use, thereby removing the old macro from use in the software. To assign the button, click on “Macro” in the Macro sub-menu (Figure 2, Step 2). This will open the Macro Control window. Select “Assign Macro to Button” (Figure 2, Step 3), then select the button that you would like to use (Figure 2, Step 4). Type in desired text that you would like to appear on the button in the “Text” area (Figure 2, Step 5). Click on the “…” button to select the Batch Export file (Figure 2, Step 6). Click Apply (Figure 2, Step 7).

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To install Batch export in ZEN software, select the Macro pull-down menu and then “Macro” to open the Macro Control window (Figure 3, Step 1). This will open the Macro Control window. Select “Assign Macro to Button” (Figure 3, Step 2), then select the entry that you would like to use (Figure 3, Step 3). Select the entry based on the number of existing macros that are already installed; meaning, if under the Macro pull-down menu there are four macros installed, select entry 5. Type in desired text that you would like to appear on the button in the “Text” area (Figure 3, Step 4). Click on the “…” button to select the Batch Export file (Figure 3, Step 5). Click Apply (Figure 2, Step 6).

Figure 2: How to assign Batch Export to a button in AIM software

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Running Batch Export macro Start the macro by clicking on the Batch Export button in AIM (Figure 4) and selecting the Batch Export entry from the Macro pull down menu in ZEN (Figure 5).

Figure 3: How to assign Batch Export to an entry in ZEN software

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Figure 4: How to start Batch Export in AIM

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Once the macro is loaded, select the “…” button to select either the .mdb folder (for AIM) or the image folder (for ZEN) (Figure 6, Step 1). To use Batch Export on a set of image files, all files must be saved to either the same .mdb folder (for AIM) or the same image folder (for ZEN). Once a .mdb folder or the image folder has been selected, the names of all image files associated with that .mdb folder or the image folder will populate in the left hand space (Figure 6, Step 2).

Figure 5: How to start Batch Export in ZEN

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Once a database or folder is selected, some or all of the images can be selected for export. Only images that are highlighted in blue will be exported. All image files can be selected by clicking on the first image file, pressing “Shift”, and then highlighting the remaining files. Or specific image files can be highlighted by pressing “Ctrl” and then using the mouse to select specific files. In Figure 6, only the first file, “cells10.lsm”, has been selected. Click “Export File Name” to select the output folder for the exported images (Figure 7). In Windows Explorer, a tag can be added to the file name. For the example shown in Figure 7, “Lab_Meeting_August2010” is entered into the File Name. Images are then exported with this tag, followed by the name of the image file. For Figure 7, the exported file would read

Shows the currently selected .mdb file or image folder

Shows the image files associated with the selected .mdb file or image folder

Shows thumbnail of highlighted image file

Allows selection of .mdb file or image folder

Figure 6: Loading a .mdb file or folder for export of images

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“Lab_Meeting_August2010_cells 2.tif”. Leave the File Name blank in order to have the exported files maintain their original names.

Figure 7: Selecting an output folder and tags for the exported file names

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There are three different options for exporting the image files: “Single image with raw data”, “Series with raw data”, and “Content of the image window” (Figure 8).

“Single image with raw data” versus “Series with raw data” refers to options for multidimensional image data, such as Z-stacks or time series. “Single image with raw data” will only export the single Z-slice or time point that was visible in the image window when the image was saved. “Series with raw data” will export multiple files, one file for each Z-slice or time point. For image files that do not contain Z-slices or time points, either of these two functions will work. When choosing either “Single image with raw data” or “Series with raw data”, you have the option to select either a red, green, or blue palette for three of the channels (Figure 9). Channels are numbered left to right, top and then bottom. For the image shown in Figure 10, Channel 1 is blue, Channel 2 is green, and Channel 3 is red. To maintain these colors in the exported image, you would need to indicate these channels as the appropriate colors. You

Figure 8: Selecting between “Single image with raw data”, “Series with raw data”, or “Content of the image window”

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could also use this opportunity to change the exported color palettes. If you do not wish a channel to export, you can select “-“ for that particular color.

Figure 9: Selecting specific color palettes for the different channels

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If “Monochrome” is selected, you will be given the option of selecting one channel (Figure 11). This channel will be exported in a grey palette.

Figure 10: In this example, Channel 1 is blue, Channel 2 is green, and Channel 3 is red. These palettes can be changed in Batch Export.

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Note that for “Single image with raw data” or “Series with raw data”, it is important that all images in the .mdb file or image folder have the same channel set up. This is because you will assign export palettes based on channel. Additionally, both of these options ignore any overlays that may have been drawn on the image, such as rulers, shapes, and/or text. If “Content of the image window” is selected, the file will be exported with the same palette as was assigned in the image and with any overlays that may have been added. It will export a single view with all channels overlayed. If “Split Screen” is selected, then the files will be exported in a split screen view (Figure 12).

Figure 11: Select “Monochrome” and choose one channel to be exported in grey palette

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Before clicking “Start Batch Export”, be sure that “Long File Names” is selected to ensure that the file names maintain their original names plus any tag you have added. “Overwrite Files” will automatically overwrite any files with the same name. These options are shown in Figure 13.

Figure 12: Select “Content of the Image Window” to have the file exported with the same palette colors and any overlays. Tick “Split Screen” to have the file exported in split screen view.

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Figure 13: Select “Long File Names” to maintain the image name and “Overwrite Files” to replace any image files with the same name. Click “Start Batch Export” to start.