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Directory Contents Panel

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Overview

Directory Contents Panel

This panel displays a list of files in the selected directory and provides the option to filter them based on known image and video formats.

Multiple buffer buttons

Buffer Buttons Popup

Multiple buffer buttons at the upper part of the panel provide fast access to several datasets stored in memory. Each button represents a dataset, and the green color indicates that a dataset is loaded in that buffer.
When you hover your cursor over a button, a tooltip with the full file name of the loaded dataset appears, helping you identify the dataset.

You can switch between datasets by clicking on the desired buffer button.

Clicking on a buffer button opens a popup menu with the following options:
  • Duplicate dataset: creates a duplicate of the currently shown dataset and places it in an available buffer.
  • Sync view, (xy) with: synchronizes the view with another dataset in XY coordinates.
  • Sync view, (xyz) with: synchronizes the view with another dataset in XYZ coordinates, for 4D-5D datasets.
  • Sync view, (xyzt) with: synchronizes the view with another dataset in XYZT coordinates, for 5D datasets.
  • Link view with: links views in two MIB buffers; shifts in one view automatically shift the other. Toggle buffers with Ctrl + E.
    Demonstration
  • Close dataset: removes the selected dataset from memory.
  • Close all stored datasets: removes all stored datasets from memory.

These buffer buttons and options provide convenient ways to manage and interact with multiple datasets in MIB.

File list box

File List Context Menu

The major part of the panel is occupied by a list box that displays files in the selected directory, chosen from the Path panel.
Files are filtered based on the specified filter. Selecting Filter: all known displays all readable formats.

Navigating folders
  • Double-clicking [.] changes the folder to the top level of the current logical drive.
  • Double-clicking [..] changes the folder to one level up.
  • Double-clicking [DIR NAME] navigates MIB into the clicked directory and shows files inside it
    (MIB_Algn folder in the snapshot)
Selecting and loading datasets
  • Double- a file loads it into MIB and displays it in the Image View panel.
  • Select individual datasets by holding Shift or Ctrl and clicking on files. Load them via the context menu ( options below).
Context menu options

File List Context Menu

The context menu, accessed with , provides these operations on selected datasets

  • Combine selected datasets: combine selected datasets into a single 3D stack.
  • Load part of the dataset (AM, TIF, BioFormats): load a specific part of a larger dataset, defining start/end points, z-step, and XY binning (available for Amira Mesh, TIF, and BioFormats-readable datasets) demo.
  • Load each N-th dataset: assemble every N-th file into a 3D stack.
  • Insert into the open dataset: insert selected files into the currently open dataset.
  • Combine as color channels: combine selected datasets into a single 2D slice, each assigned to a color channel.
  • Add as a new color channel: add images as a new color channel to the existing dataset. Select channels in the View Settings panel.
  • Add each N-th dataset as a new color channel: add images with an N-step as a new color channel to the existing dataset.
  • Rename selected file: rename the selected file.
  • Delete selected files: permanently delete selected files from the disk.
  • File properties: show file details like date/time and size in bytes.

Note

above the scroll bar scrolls the list to the top.

Filter

Filter Dropdown

The Filter dropdown allows filtering the file list based on available image type filters.
Available extensions depend on whether the standard or Bio-Formats reader is used and if virtual mode is enabled, resulting in four filter configurations.

Modify extensions in the filter list

Register TIF as an extension available for the BioFormats reader in the standard mode

To modify file extensions the list of filters:

  • click over Filter.
  • Choose an option:
    • Register extension: add extensions to the filter list.
    • Remove selected extension: remove a selected extension from the filter list.

Update button

The Update button refreshes the file list in the Directory Contents panel.

Left interchangeable panels

Left interchangeable panels

The selected panel appears in the lower-left part of MIB:

Right interchangeable panels

Left interchangeable panels

The selected panel appears in the bottom-right part of MIB:

Bio checkbox

When Bio is checked, the Bio-Formats reader loads datasets.
MIB supports specific biological image formats (native to various microscopes) via the Bio-Formats Java library, stored in the MIB\ImportExportTools\BioFormats directory.

Note

Performance of the Bio-Formats reader may be slower than standard native readers due to Java-related overheads.

Help button

The ? button links to this help page.

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