Loading Files

Loading via the File Button

  1. Click the + button at the top of the Data tab in the left sidebar.
  2. The native file browser opens.
  3. Select one or more supported files and click Open.
  4. Nexus parses the files and displays the imported signals in the Data tab.

You can select multiple files at once. Each file is parsed according to its extension - for some formats (for example, different CSV-based formats), Nexus also performs content-based auto-detection to distinguish between file variants. See Supported File Formats for the full list.

Drag and Drop

Drag files from your operating system’s file explorer and drop them directly onto the Nexus window. Nexus detects the file extension and imports them the same way as the file button.

Merging Multiple DM3/DM4 Files

When you select two or more DM3 or DM4 files at once, Nexus presents a dialog with two import options:

Separate Datasets

Each file is loaded independently as its own dataset. Use this when the files contain unrelated measurements.

Example: Selecting 5 DM4 files → 5 separate datasets, each with their own signals.

Combined Image Series

Images with the same pixel dimensions across all selected files are merged into a single time-series signal. Spectra (1D signals) are kept as individual signals. Use this when files were captured sequentially during an experiment, such as a series of HRTEM images at different time points.

Example: Selecting 5 DM4 files, each containing one 1024×1024 image → 1 image series with 5 frames.

Only images with matching width and height are merged. If files contain images of different sizes, each dimension group becomes its own series. Spectra are never merged.

The merged dataset name is derived from the common filename prefix of the selected files. Frame timestamps are taken from each file’s acquisition metadata when available.

How it works

  1. Click the + button in the Data tab.
  2. Select multiple .dm3 or .dm4 files in the file browser.
  3. The Import DM3/DM4 Files dialog appears.
  4. Choose Separate Datasets or Combined Image Series.
  5. The files are loaded according to your selection.

Merging Multiple EMD Files

When you select two or more Velox EMD files at once, Nexus presents the same merge dialog:

  • Separate Datasets — Each file loads independently.
  • Combined Image Series — Images with matching dimensions are merged into a single time-series signal. Different detectors (e.g. HAADF, BF) each produce their own merged series.

The merged dataset name is derived from the common filename prefix. If the prefix is very short, the parent folder name is used instead.

Merging Multiple SER Files

When you select two or more TIA SER files at once, Nexus presents the same merge dialog:

  • Separate Datasets — Each file loads independently.
  • Combined Image Series — Images with matching dimensions are merged into a single time-series.

If you select both .ser and .emi files together, the .emi files are automatically excluded from separate loading since they are metadata companions to .ser files. Only the .ser files appear in the merge dialog.

Loading SenseAI TIFF Files

When you select two or more SenseAI TIFF files, Nexus presents a dialog with two import options:

  • Individual — Each file is loaded as a separate dataset.
  • Time Series — All files are merged into a single 2Dts image series, ordered by their filename timestamps.

SenseAI TIFF files are identified by the capture_ filename prefix. Each file may contain up to four pages (reconstruction, import, reference, mask). Timestamps are extracted from the filename pattern.

GMS In-Situ Dataset Auto-Detection

When you select a single DM3 or DM4 file that belongs to a Gatan Microscopy Suite (GMS) In-Situ dataset, Nexus automatically detects the full dataset.

How detection works

Nexus uses three detection strategies:

  1. Folder structure - If the file is inside a folder hierarchy like Hour_XX/Minute_XX/Second_XX/, Nexus navigates up to the dataset root and discovers all DM files in the structure.
  2. In-situ metadata tags - If the DM file contains In-situ tags in its metadata (a master file), Nexus scans the surrounding directory for related files.
  3. Same-folder series - If the selected file’s folder contains multiple DM files sharing the same naming prefix with sequential numbers (e.g. sample_0315.dm3, sample_0318.dm3, sample_0319.dm3), they are detected as a series.
  4. Same-folder fallback - If there are multiple DM files in the same directory but they don’t share a common prefix (e.g. different magnifications like sample_600X_0001.dm3 and sample_1500X_0003.dm3), all DM files in the folder are offered as a dataset.

What happens when a dataset is detected

The behavior depends on the detection method:

  • Master file (In-situ tags): The entire dataset is automatically loaded as a merged time series with no popup. This is the most common case for GMS In-Situ experiments where the master file contains experiment metadata.
  • Folder structure or same-folder series: A prompt dialog appears asking “This file is part of a larger dataset. Would you like to load the full dataset?” You can choose:
    • Yes — Load all discovered files as a combined time series.
    • No, load selected file only — Load just the file you originally selected.

If the selected file is not part of a GMS dataset, it is loaded normally without any prompt.

Timestamps from folder paths

When DM metadata timestamps are not available, Nexus extracts timestamps from the GMS folder hierarchy:

  • Hour_XX → hours component
  • Minute_XX → minutes component
  • Second_XX → seconds component
  • _Frame_NNNN in filenames → sub-second ordering

Loading Progress and Notifications

When files are being loaded, Nexus displays a progress indicator. Once loading is complete, a toast notification appears in the lower-right corner confirming success (with a signal count) or reporting any errors with a descriptive message.