O pening Files w ith LOCI Bio - Formats

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Other file types, particularly proprietary formats that contain batches of images such as OpenLab .LIFs, Leica .LEI and .LIF and SlideBook .SLD files, can be opened using the LOCI Bio - Formats plugin.

Software

Created by Christine Labno
University of Chicago
Integrated Light Microscopy Core
Page 1 of 2
Opening Files with LOCI Bio-Formats
Certain file types, such as .TIF, .STK (.tif stack), .JPG, .GIF, .BMP (bitmap) and
DICOM files can be opened in ImageJ either using File  Open and choosing the file to
be opened, or by dragging the file or group of files onto the top of the ImageJ toolbar.
Other file types, particularly proprietary formats that contain batches of images such as
OpenLab .LIFs, Leica .LEI and .LIF and SlideBook .SLD files, can be opened using the
LOCI Bio-Formats plugin.
1) To use LOCI, you must first install it in your ImageJ plugins folder. To do this, either
go to the microscopy server, find the ~Image J  Plugins folder (it is the very first folder
in the list) and copy the whole Bio-Formats folder into your Image J  Plugins folder, or
download the stable build from the OME website: www.loci.wisc.edu/ome/formats.html
and install into your ImageJ  plugins folder.
2) Once Bio-Formats is installed, start ImageJ. Choose Plugins  LOCI  Bio-Formats
Importer. A new window will appear, prompting you to point to the file to be opened. In
this example, we are opening a Leica .lei file.
3) Once you have selected the file to be opened,
you may have to wait a few seconds while the
software reads the data. You may also be asked
to confirm the name and filepath of the file you are
opening.

Created by Christine Labno
University of Chicago
Integrated Light Microscopy Core
Page 2 of 2
4) When the Import Options window
opens, you can choose how you
want your data to be displayed.
The safest option is to choose
Standard ImageJ and leave all other
options unchecked. If you cannot
see an image in your file when it
opens, try checking “autoscale.” To
learn more about the other options,
hover over any option and
information about that option will be
displayed at the bottom of the
window.
When you have set the display the
way you want it, click OK.
5) After a few more seconds, a new window will appear with the names and thumbnails
of all the images/image stacks in the file.
Choose which image(s) or stack(s) to open by
clicking on the checkbox next to the name.
The first image is always set to open, but you
can undo this.
Keep in mind, the more images you set to
open, the longer it will take to import all the
data.
Your data will then open as images or stacks
that can be modified and saved as individual
.TIF or .TIF stack files.

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O pening Files w ith LOCI Bio - Formats

1. Created by Christine Labno University of Chicago Integrated Light Microscopy Core Page 1 of 2 Opening Files with LOCI Bio-Formats Certain file types, such as .TIF, .STK (.tif stack), .JPG, .GIF, .BMP (bitmap) and DICOM files can be opened in ImageJ either using File  Open and choosing the file to be opened, or by dragging the file or group of files onto the top of the ImageJ toolbar. Other file types, particularly proprietary formats that contain batches of images such as OpenLab .LIFs, Leica .LEI and .LIF and SlideBook .SLD files, can be opened using the LOCI Bio-Formats plugin. 1) To use LOCI, you must first install it in your ImageJ plugins folder. To do this, either go to the microscopy server, find the ~Image J  Plugins folder (it is the very first folder in the list) and copy the whole Bio-Formats folder into your Image J  Plugins folder, or download the stable build from the OME website: www.loci.wisc.edu/ome/formats.html and install into your ImageJ  plugins folder. 2) Once Bio-Formats is installed, start ImageJ. Choose Plugins  LOCI  Bio-Formats Importer. A new window will appear, prompting you to point to the file to be opened. In this example, we are opening a Leica .lei file. 3) Once you have selected the file to be opened, you may have to wait a few seconds while the software reads the data. You may also be asked to confirm the name and filepath of the file you are opening.

2. Created by Christine Labno University of Chicago Integrated Light Microscopy Core Page 2 of 2 4) When the Import Options window opens, you can choose how you want your data to be displayed. The safest option is to choose Standard ImageJ and leave all other options unchecked. If you cannot see an image in your file when it opens, try checking “autoscale.” To learn more about the other options, hover over any option and information about that option will be displayed at the bottom of the window. When you have set the display the way you want it, click OK. 5) After a few more seconds, a new window will appear with the names and thumbnails of all the images/image stacks in the file. Choose which image(s) or stack(s) to open by clicking on the checkbox next to the name. The first image is always set to open, but you can undo this. Keep in mind, the more images you set to open, the longer it will take to import all the data. Your data will then open as images or stacks that can be modified and saved as individual .TIF or .TIF stack files.

O pening Files w ith LOCI Bio - Formats

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O pening Files w ith LOCI Bio - Formats