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Saving the Dataset and Projections

At any time you may choose to save the current dataset. Note that the dataset is saved as it exists in its current state, not as it existed when it was first opened. In other words any changes to the dataset by image processing filters are present in the saved image. The saved volume is also affected by the currently visualized R.O.I.

Select the menu item File >> Save Image... to bring up the following window.

Saving Datasets

Select the destination directory by either typing the path or using the browse button. The dataset can be saved as either a 2D sequence of files or a single 3D file. The bit-depth of the image can also be adjusted but the use of this feature is discouraged as it may result in loss of precision or unnecessary increase in file size. The Save as Series check box controls this option. Also of lesser importance is the Pad with Zeros check box. If the file name is NOT padded with zeroes, than the lexicographical ordering of the files may not reflect the true Z position of the files. NeuronStudio can correctly read the image series even if the lexicographical ordering is not correct though. Note that the file names are updated and displayed in the window to make it easy to check that the names are correct prior to saving.

TIP: If the size of your dataset exceeds the maximum file size for your machine, you will have to select Save as Series.

In addition to saving the dataset, you may want to save the projections at some point. The projections will be saved as they currently exist with any changes due to image processing filters. However, the projections will always be saved in their original pixel format. In other words any artifical coloring due to e.g. the palette will not be reflected in the saved images. As with saving the dataset, the saved projections depend on the currently visualized R.O.I.

Select the menu item File >> Save Projections... to bring up the following window.

Saving Projections

The procedure for saving the projections is almost identical to the dataset except that the check box options are no longer applicable (see above). Select the destination directory by either typing the path or using the browse button. The file names are updated and displayed in the window to make it easy to check that the names are correct prior to saving.

TIP: TIFF is a well-established image file format. Choose RAW if you want to save the images as a block of pixels containing no additional information.

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Send questions or comments to: alfredo.rodriguez@mssm.edu