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Hi Giovanni,
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<div class="">thanks for your quick response. Yes, that did the trick. Sorry, I should have caught that myself using the recorder. Thanks a lot for your help!</div>
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<div class="">best,</div>
<div class="">Andy<br class="">
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<div class="">On 12 Feb 2019, at 13:11, Cardone, Giovanni <<a href="mailto:cardone@biochem.mpg.de" class="">cardone@biochem.mpg.de</a>> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi Andy,<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">I think that you should try to include the full name of the file between square brackets. I didn’t try for this specific command, but this is the common practice
when file names contain spaces (otherwise the script interpreter reads only the substring before the space).<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">run(“Bio-Formats”, “open=[/path/to my/file]”);<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">I hope it helps,<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Giovanni<o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]<span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Clark Andrew<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Dienstag, 12. Februar 2019 13:02<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>[ome-users] FIJI bio-formats importer cannot open paths with spaces (from macro)<o:p class=""></o:p></span></div>
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There’s a small issue with calling the bio-formats importer from a FIJI macro. It will not open a file if there is a space anywhere in the file path. For example:<o:p class=""></o:p></div>
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run(“Bio-Formats”, “open=/path/to my/file”);<o:p class=""></o:p></div>
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will raise the following error:<o:p class=""></o:p></div>
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The specified file (/path/to) does not exist.<o:p class=""></o:p></div>
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I tried replacing the spaces with “\ “ or putting the filepath in double quotes, but I get the same error.<o:p class=""></o:p></div>
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This is on a freshly updated FIJI and bio-formats on OSX. There is no problem opening the file using the Bio-Formats importer from the dropdown plugins menu, only running it from a macro script.<o:p class=""></o:p></div>
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Thanks!<o:p class=""></o:p></div>
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andy <o:p class=""></o:p></div>
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<span style="" class="">____________________<br class="">
Andrew G. CLARK, PhD<br class="">
Postdoctoral Fellow<br class="">
VIGNJEVIC Group<o:p class=""></o:p></span></div>
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+33 (0) 156 24 67 70<br class="">
<a href="mailto:andrew.clark@curie.fr" style="color: purple; text-decoration: underline;" class="">andrew.clark@curie.fr</a><o:p class=""></o:p></span></div>
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<span style="" class=""><a href="http://www.andrewgclark.info/" style="color: purple; text-decoration: underline;" class="">www.andrewgclark.info</a><o:p class=""></o:p></span></div>
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<span style="" class="">Institut Curie / UMR 144<br class="">
12, Rue Lhomond<br class="">
75005 Paris<br class="">
FRANCE<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">ome-users
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class="">____________________<br class="">
Andrew G. CLARK, PhD<br class="">
Postdoctoral Fellow<br class="">
VIGNJEVIC Group</div>
<div class=""><br class="">
+33 (0) 156 24 67 70<br class="">
<a href="mailto:andrew.clark@curie.fr" class="">andrew.clark@curie.fr</a></div>
<div class=""><a href="http://www.andrewgclark.info" class="">www.andrewgclark.info</a></div>
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<div class="">Institut Curie / UMR 144<br class="">
12, Rue Lhomond<br class="">
75005 Paris<br class="">
FRANCE</div>
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