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--- 1_0:import_images [2017/04/10 13:57]
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+++ 1_0:import_images [2020/10/22 16:28] (current)
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 ====== Import images and movies ======
-{{ :1_0:importscreen.png?600 |Import Screen}}
+The import procedure involves copying raw data files into the project directory, assigning and determining a set of parameters for each image, and optionally running one or several scripts for each image during and/or after import. This process is handled by the Import Tool. The tool can be configured to automatically fetch newly recorded stacks throughout the microscopy session from a network-mounted storage location. A delay timer can be set to ensure that files are only copied after being fully written by the camera computer. Files can optionally be deleted from the camera computer after import.
+{{ :1_0:importscreen.png?800 |Import Screen}}
+===== What can be imported? =====
+Using the tool, image data can be imported as dark-subtracted and gain-corrected images, or as dark-subtracted images only (in this case a separate gain reference file should be provided). Optionally, combinations of raw image stacks, drift-corrected stacks, and drift-corrected and averaged 2D images, can be imported simultaneously.
+===== How do I import images from EPU's file structure? =====
+EPU is the automated data acquisition software from FEI / ThermoFisher. EPU saves recorded movies grouped by the grid-square that the images were recorded from.  EPU creates for each grid-square one sub-folder, and within a subfolder called "Data". Images recorded from that grid-square are then placed into the "Data" sub-folder as MRC files, together with an XML file that contains some basic information about the image.
+If you activate the button "Import is from EPU", the Import panel will take this EPU file structure into account. You can set the default state of this button in the program preferences panel.
+===== How do I import images from other file structures ? =====
+If you do not activate the button "Import is from EPU", then import from other packages such as SerialEM or EMMenu (TVIPS) or Lattitude (Gatan) is assumed. In this case, images are expected to reside in a sub-folder indicated in the "Import From" panel. It is possible to import several different files for one image simultaneously, by placing corresponding files into different subfolders and specifying their names in the "Import From" panel. This would be useful, for example, if you have raw stacks (movies), drift-corrected stacks, and 2D averaged image files for each datafile, and want to maintain all of these during import.
+===== Processing imported images =====
+The Import Tool allows a choice of scripts to be run on the imported data during import, which results in sequential processing of the data. This is required, e.g., if the incremental electron dose on the sample has to be computed for consecutively recorded image stacks within the same dose-fractionated tomography tilt series. The Import Tool also allows a choice of scripts to be submitted to the parallel batch queue for processing after import. This would be used, e.g., to schedule computationally intensive tasks such as motion correction and the subsequent steps.