Data Analysis

The raw data are automatically copied from the detector to the analysis computer (one of the tomo cluster computers) under the folder /data2/YYYY-MM/YYYY-MM-PI_lastName.

Manual

To manually reconstruct a data set, use the tomocupy cli tool.

[2bmb@tomo4,~]$ bash
[2bmb@tomo4,~]$ conda activate tomocupy

then for help:

[2bmb@tomo4,~]$ tomocupy recon -h

To do a test reconstruction type:

[2bmb@tomo4,~]$ tomocupy recon --file-name /local/data/YYYY-MM/PI_lastName/file.h5

Slides

To publish reconstruction snapshots and experiment metadata to a Google Slides presentation, see the tomolog documentation.

At your home institution

See the tomocupy documentation for installation and usage instructions.