General considerations

The most important factor for the quality (and also speed) of the alignment is the actual spacing (thickness + discarded sections) between consecutive sections. E.g., if sections are cut at 10 um then a good alignment can only be expected up to a resolution of 1 um/pixel, which corresponds to approx. 10x magnification.

Voloom basically covers two different workflows:


Interactive workflow

The interactive workflow is well-suited for users who are interested in specific sub-regions of the overall data set. These regions of interest (ROIs) don't have to be known or selected in advance. But they should not be larger than about 300 x 300 pixels  (i.e. Voloom's main window in its original size) to achieve a sufficient accuracy using a locally rigid alignment.

  • The upside here is that there is almost no waiting involved since step 5 of the reconstruction wizard can be skipped and export can be performed using the "Rigid (Faster)" setting for "Alignment".
  • The downside is the limited size of the ROI that is to be analyzed and/or exported and that the export resolution is limited to 4 times the currently visualized resolution. (This is a built-in limitation since a rigid transformation couldn't possibly yield a good alignment for larger areas at a higher resolution.)

Batch-mode workflow

The batch-mode / full-resolution workflow is solely intended for users who absolutely need a large or even the full area of the data exported for further analysis. Sometimes, users can't choose their ROIs before exporting from Voloom, e.g. in case they want to run high-resolution analysis on the whole dataset in order to collect and measure cell shapes over the whole data set. In this scenario, it is advisable to batch align the whole data set in step 5 of the reconstruction wizard up to 1:4 or 1:2 resolution and then export the data using the "Deformable" setting in the export dialog.

  • Upside: Having good alignment over large areas (> 500 x 500 pixels) of the data
  • Downside: Extra wait times for batch alignment in step 5 as well as during the deformable export.