Opening multiple TIF files in folders

The Open folder of TIF files main menu item or the TIF folder type in the open dialog allows to explore and read files in a single folder or in a folder structure as a multi-dimensional data set. The Multi-Dimensional Open dialog will appear with the TIF folder tab active (unless the Scan automatically next time is checkmarked as default in this tab). The organization of the files in the folder(s) is described by a rule or pattern. The dialog will look for any file that matches the selected rule in the folder, and recursively in subfolders. The built-in rules can be chosen as an explanatory named rule, corresponding simple rule comprising of fixed text, fields and wildcards, or a regex (regular expression) pattern to also provide unlimited flexibility and complexity. Custom simple and regex rules can be added by the user.

TIF files:

• monochromatic TIF files (8-32 bit, uncompressed or LZW compressed, PC or Mac)
• 24-bit RGB TIF files
• Single plane TIF files, or TIF stacks containing a Z-series, e.g. Metamorph STK files
• The extension does not have to be TIF, it is encoded in the rule
• The time axis is reconstructed from standard TIF metadata is present.

Multiple dimensions - rules or patterns below describe fields within the folder and file names that encode:

• Data sets - recordings that will be concatenated during open (currently only in time)
• Positions - stage positions or microplate wells
• Channels
• Time points
• Z-position - currently only the first z-position is opened.

Constraints:

• Image Analyst MKII allows only image series with equal x,y,t dimensions to be opened as linked image windows, therefore image series with differing dimension will be opened unlinked.
• All 3 channels of RGB images will be open without choice

Rules and patterns:

• Named rules - these are for generic use, for few specific formats, and also serve examples for simple rules and regex patterns
  • All TIF files as positions
  • All TIF files as frames
  • TIF files named with channel and time point
  • TIF files in folders named with channel and time point: folders will be assumed as positions
  • BD Pathway: data are organized in folders named as 'Well *' and named as channel name and time point. Numerator and denominator channels are opened as separate channels, available for ratiometric processing.
  • Metafluor:  for the numeric extensions (*.001 to *.999 followed by *.1000). Note: open INF files instead to read the correct time axis.
  • Metafluor with alphanumeric extensions: (*.001 to *.999 followed by *.0AA). Note: open INF files instead to read the correct time axis.
  • Metamorph
• Simple rules - build your own rule to load a multi-dimensional TIF data set of an arbitrary file naming convention.
  • A simple rule comprises of fixed characters that must be present in all files, fields identifying dimensions, and wildcards.
  • Fields (not case sensitive; all fields are optional; maximum one field for each dimension):
    • Data sets: %dataset% (synonyms: %name%)
    • Positions:
      • as text: %position% (synonyms: %xy%)
      • as number: %positionnumber%
      • as well name in the letter+number+number format: %well%
    • Channels
      • as text: %channel% (synonyms: %ch%, %wavelength%)
      • as number: %channelnumber%  (synonyms: %wavelengthnumber%)
    • Time points
      • as text: %frame% Note: these will be alphabetically ordered to load the time course
      • as number: %time% (synonyms: %t%) Note: these will be ordinally ordered to load the time course
    • Z-position - currently only the first z-position is opened.
      • as number: %z%
  • Wildcards:
    • Any character including none: *
    • A single digit: %number%
    • Any number of digits, but at least one: %numbers%
    • A single letter: %letter%
    • Any number of digits, but at least one: %letters%
    • A single character: %character%
    • Any number of characters, but at least one: %characters%
  • Examples for simple rules:
    • All TIF files as positions : %position%.tif
    • All TIF files as frames : %frame%.tif Note: this will provide a single time series
    • TIF files named with channel and time point: %channel%%time%.tif
    • TIF files in folders named with channel and time point: %position%\%channel%%time%.tif
    • Metamorph: %dataset%_w%channel%_s%position%_t%time%.*
• Regex patterns - this is for advanced use only.
  • You may start with a named or simple rule, then translate it to regex by simply switching to regex pattern and modify it.
  • Define named capturing groups using the above field names as (?<field name>regex expression comes here)
  • Get help here to build your regex: e.g.: www.regex101.com (use pcre)