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RT @xuepan3: @palankarr @manorlaboratory Hi Raghva, We compared the results generated by IMARIS and Trackmate in ImageJ. There are some min…
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

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RT @albertcardona: Plotting from your @FijiSc #python scripts, using ImageJ's internal plotting library, and with @jfreechart for prettier…
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

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RT @CefapConfocal: If you struggle with image analysis, check our webpage with few ImageJ and Zen tutorials: https://t.co/9ExHi8MkL1 ps .:…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

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RT @iefforts: The cells were visualized on a Nikon AR1 or Leica SP8 confocal microscope. At least 30 cells were analysed for each condition…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

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RT @MarJungle: BigStitcher on ImageJ for 3D model reconstructions. A beta-version is available via the Fiji Updater. I am going to try this…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

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RT @ARVOtvst: New in the August issue: 25-MHz ultrasound biomicroscopy combined with #ImageJ software can be used to evaluate the opacity d…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)
downloads:pefileto3dstacks

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 (ImageJ, upgrade page).

Installation

Download 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 byPerkin-Elmer Loader (E. Seitz, ALMF) to 3D stack time series (multiple 3D stacks) for 3D tracking using “Manual Tracking” plugin.

Perkin-Elmer Loader (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 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 Manual Tracking Plugin: Use the “Projection2D.tif” for the tracking in xy plane.

4. In 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.

downloads/pefileto3dstacks.txt · Last modified: 2016/05/24 05:46 (external edit)