4.3 Vertical Sections.
This is a type of z-series that produces optical equivalent of a 2-dimensional cross-section through your
sample. A series of scans are collected along a single line while incrementing the focus between each
line. The resultant image represents a vertical “slice” taken through the volume where the first (top) line
of the image represents the top of the volume and each successive line represents a line scanned at
successive depths through the volume.
1. Determine the extent of the volume to be collected, as described above;
2. Set the necessary z-step increment, as described in section 4.2;
3. Scan an image at some level displaying structures to guide orienting the line;
4. Select the ‘Line’ scan region, Figure 6.3;
5. Draw the line across the image in any desired orientation;
6. The line may be re-positioned in x,y and position of its ends;
7. Move to the XY acquire button, Figure 4.7;
8. Select ‘Depth, Figure 4.7;
9. Click on the XY acquire button to collect the z-series, Figure 4.7;
5. Files: Saving and Transferring
5.1 Saving Files
Olympus created 2 proprietary file formats for images collected on their confocal microscopes. Both
formats record all meta-data, regions of interest and preserve the original 12-bit (4096) image intensity
values. Each format has its benefits and drawbacks.
5.1.1 The Olympus “OIB” format.
This format writes all images and meta-data to a single file. Some software applications, such as
Slidebook for Windows, Imaris (Bitplane) and the LOCI plugin for ImageJ have incorporated the ability
to read the .oib format. The OIB format is not widely supported. If you do not have software to open
this format, your images cannot be accessed.
5.1.2 The Olympus “OIF” format.
Each acquisition saves both a folder and a file. The naming convention is “filename.oif.files” and
“filename.oif”, respectively. The “filename.oif” is a text file containing metadata. The directory
“filename.oif.files” contains the images as a series of16-bit TIFF images, one image for each channel in
each plane of focus, timepoint or lambda scan. The directory also contains an additional “filename.pty”
file with metadata regarding the individual TIFFs and some additional non-image files.
The “.oif” format, can be imported in the greatest range of software. It also is compatible with spooling
files to disk. It can be opened by Slidebook for Windows, Imaris, ImageJ, LOCI and Huygens.
Olympus Fluoview-1000 User’s Guide
V.M. Bloedel Hearing Research Center, Core for Communication Research
Center on Human Development and Disability, Digital Microscopy Center
May 11, 2011 26
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