[ome-users] Enquiries of opening multiple OIF files in mac via fiji

[Glen MacDonald]

Hello Fei Yang,
First, are your versions of Java and Fiji up to date?
Bio-Formats plugin is bundled with Fiji and no installation should be needed.  You can turn on the Bio-Formats update site in the Fiji updater if you always want the latest updates in B-F rather than wait for them to be bundled with Fiji updates.  

Try Fiji’s builtin Batch  processor, Process>Batch.  Documentation is in the ImageJ Manual, https://imagej.nih.gov/ij/docs/guide/146-29.html#toc-Subsection-29.12


place your OIF files and their folders in an input folder
create an output folder
Batch>Convert:
Select the Input and Output folders
Output= TIFF gives 16-bit images
Interpolations = None
Scale = 1
Read images using Bio-formats

Actually, firstly import a file using Bio-Formats to select its desired settings, e.g. Color Mode =Composite, these setting will be used by the batch processor.  Now, go ahead to run the batch process.

If you want to perform other operations on the images, run the macro recorder as you do so to record the commands, such as  Image>Color>Channels Tool to select the channels in the Composite images and set their color, or Image>Type to convert to RGB, etc.  Then place those commands in the Batch>Macro option.

I also have a macro that I can send to you that batch processes OIF files to open, convert to tiff, create projections.  

You may want to send future questions regarding Fiji and Bio-Formats to the ImageJ listserver or the Fiji discussion forum.

 Regards
Glen MacDonald
Digital Microscopy Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
(206) 616-4156
depts.washington.edu/digmicro
glenmac at uw.edu

> On Jun 6, 2017, at 1:24 AM, Fei Yang Tan <t.feiyang1997 at gmail.com> wrote:
> 
> Hi to whomever it may concern,
> 
> I would like to ask how to open multiple oif files in mac via fiji.
> I tried to no avail, I also tried installing LOCI and Bioformat plugins, but it didn't work.
> Please advise. Thank you.
> 
> Warmest Regards,
> Fei Yang
> 
> 
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