Open Image Sequences

or 'Open Image with Bio-Formats' menu items in the File main menu, the Toolbar button, or drag and drop files on the main window. Open results one or more Image Windows or a  Multi-Dimensional Open Dialog. All file open operations are read only, Image Analyst MKII does not alter the original data files.

Image Analyst MKII uses its internal speed optimized code to read TIFF, LSM, STK, ND, ND2 and AVI. These, and in addition many other formats can be opened using the Bio-Formats open source reader by selecting (USE BIO-FORMATS (*.*)) as file type in the Open dialog, or using the 'Open Image with Bio-Formats' main menu point. However the Bio-Formats reader is slower and has a larger memory use than the internal reader. Results obtained with the Bio-Formats reader depend on the actual version of BIO-FORMATS and the file type. Files dropped on the main window will be opened with the last used method (internal reader or Bio-Formats)  or using Bio-Formats if no internal reader is available to open that file. This behavior can be changed using the 'Set Folder Locations and Default Open Method' File main menu item.  If you encounter an error message when trying to use Bio-Formats open, you may need to install Java or Microsoft Visual C++ 2010 Redistributable Package x86. See download links here.

Image Analyst MKII opens as a single image sequence the following formats:

• Metamorph stack files (*.stk), 8 or 16 bit grayscale, uncompressed or LZW compressed
• TIFF stacks (*.tif) 8 or 16 bit grayscale, uncompressed or LZW compressed, PC or MAC format
• Set of TIFF files by using multiple files selection in the open dialog

Image Analyst MKII opens as  multiple image sequences as channel by channel the following formats:

• RGB 24 and 48 bit TIF files open as three separate image windows corresponding to red, green and blue channels
• Metafluor experiments (*.inf), each channel results a separate image window
• Zeiss LSM (*.lsm),  8 to 16 bit grayscale, uncompressed or LZW compressed each channel results a separate image window, unless 'Zeiss LSM Multi Time Series' is selected as file type (see below).
• AVI (*,avi) video files opened as separate channels for red, green and blue. The corresponding video codec needs to be installed on the system.

The Multi-Dimensional Open Dialog appears when opening:

• Metamorph Multi-DimensionalAcquisition (*.nd files)
• Nikon Elements N-dimesnional Acquisition (*.nd2 files)
• Zeiss LSM Multi Time Series (*_Sum.lsm files)
• All file formats opened by Bio-Formats
• When selecting multiple files their content will be merged in time.

Linkage:

• When multiple channels are opened, the resultant image windows will be linked, therefore available for processing in the same context.

Time scale:

• Metafluor *.inf precise (~10ms) time information is obtained from the inf file. Only frames after the last 'Zero clock' are opened
• Metafluor *.stk files, and *.nd data sets consisting *.stk files will have precise (ms) time information, relative to the first frame. When multiple nd files are merged, the time scale will be still absolute to the first frame.
• Metafluor *.tif files result only 1s  precise time scale.
• Nikon Elements *.nd2 files have precise timing, when merging multiple nd2 files the precise time passed between two files is accounted for. Additional timing information (resolving timing of each lambda channel) can be obtained by reading event marks in the ND2 Tweak tab of the Multi-Dimensional Open Dialog.
• Zeiss *.lsm files have accurate timing
• Bio-Formats time stamps are obtained from the OME tags or in the absence of time stamps using the acquisition date stamps.