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Re: Opening Stack with ImageJ and BioFormats

Posted by Herbie on Oct 30, 2019; 10:28am
URL: http://imagej.273.s1.nabble.com/Opening-Stack-with-ImageJ-and-BioFormats-tp5022585p5022616.html

Thanks Stein and Wayne,

for insisting on my initial suggestion of not allowing slashes and
colons in file names and for implementing the code change!

Regards

Herbie

::::::::::::::::::::::::::::::::::::::::::
Am 29.10.19 um 20:22 schrieb Stein Rørvik:

> I don't understand why spaces in labels are no longer allowed in this case?
> Spaces should be valid in filenames for all the relevant operating systems in use for ImageJ.
>
> It would make more sense to disallow the colon character ":" in addition to forward "/" and also backward "\" slashes, to avoid problems with the image title to filename conversion.
>
> Stein
>
> -----Original Message-----
> From: ImageJ Interest Group <[hidden email]> On Behalf Of Wayne Rasband
> Sent: 29. oktober 2019 16:40
> To: [hidden email]
> Subject: Re: Opening Stack with ImageJ and BioFormats
>
>> On Oct 28, 2019, at 5:19 AM, Herbie <[hidden email]> wrote:
>>
>> Dear experts,
>>
>> a current discussion here on the ImageJ-list leads me to post a question about opening stacks either with "Plain ImageJ" or by using "Bio-Formats Importer" from plain ImageJ.
>
> This bug is fixed in the latest ImageJ daily build (1.52s1). The “Stack to Images” command no longer uses the slice label as the file name if it contains a forward slash or space.
>
> -wayne
>
>> Attached please find a test-stack consisting of two color channels.
>>
>> 1. "Plain ImageJ"
>> (Copy the following macro code lines to an empty macro window "Plugins
>>>> New >> Macro" and run it.) ///// open(""); // please open the
>> test-stack run("Stack to Images"); ///// I get two images with titles:
>> "confocal-series_2Ch-0001"
>> "confocal-series_2Ch-0002"
>>
>> 2. "Bio-Formats Importer" from plain ImageJ (Copy the following macro
>> code lines to an empty macro window "Plugins >> New >> Macro" and run
>> it.) ///// f=File.openDialog(""); // please open the test-stack
>> run("Bio-Formats Importer", "open="+f+" color_mode=Default
>> rois_import=[ROI manager] view=[Standard ImageJ]
>> stack_order=Default"); run("Stack to Images"); ///// (Please take care
>> of possible line breaks introduced by the mailer.) I get two images
>> with titles:
>> "c:1/2 - confocal-series_2Ch"
>> "c:2/2 - confocal-series_2Ch"
>>
>>
>> The latter images appear in the Mac-Finder, when saved as TIF, with file names:
>> "c/1/2 - confocal-series_2Ch.tif"
>> "c/2/2 - confocal-series_2Ch.tif"
>>
>> For magic reasons the latter image files are correctly opened on my Mac by using the macro:
>> (Copy the following macro code lines to an empty macro window "Plugins
>>>> New >> Macro" and run it.) ///// f=File.openDialog(""); // please
>> open one of the result images open(f); ///// I get the images opened
>> by plain ImageJ with titles:
>> "c:1:2 - confocal-series_2Ch.tif"
>> "c:2:2 - confocal-series_2Ch.tif"
>>
>> This may be judged as being nice but I judge it highly confusing.
>>  From my point of view the prefix introduced by "Bio-Formats Importer" appears being far from reasonable.
>>
>> Thanks for reading and testing!
>
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