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Hi Hitesha,
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<div class="">When converting from Leica SCN to TIFF you are probably going to see a large jump in file size. From your output you seem to being using LZW compression which should help reduce the output size somewhat but it will still be larger than the original. </div>
<div class="">I suspect the errors when attempting to read the files may be due to memory constraints but we would need to test the file to confirm. If you are able to upload the original scene file to <a href="https://www.openmicroscopy.org/qa2/qa/upload/" class="">https://www.openmicroscopy.org/qa2/qa/upload/</a> then
we can check and confirm if the generated tiff is indeed valid or if there has been an issue during conversion.</div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<blockquote type="cite" class="">
<div class="">On 11 Dec 2018, at 20:50, MS2016007 Hitesha Mukherjee <<a href="mailto:hitesha.mukherjee@iiitb.org" class="">hitesha.mukherjee@iiitb.org</a>> wrote:</div>
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<div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; font-size: 12pt; font-family: Calibri, Helvetica, sans-serif;" class="">
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="" class=""> Hello Team,</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class=""><br class="">
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="" class=""></span><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class="">I have been trying Bio-Formats to convert my image which is in scn format </span><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class="">(Leica
scn) using the command line bftools.zip. I have received Converted TIFF</span><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class=""><span class="Apple-converted-space"> </span>files which are huge in size (6GB and 4 GB respectively) </span><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class="">as
compared to the original .scn file (300 MB</span><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class=""> ) . The images do not open at all in any specialized <span style="font-family: 'Times New Roman', Times, serif; font-size: 14.6667px;" class="">software. </span></span><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class="">Details
of the error are </span><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class="">as follows:</span></div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class="">bftools
latest version : </span><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class="">A bundle o</span></span><span style="font-family: 'Times New Roman', Times, serif; font-size: 11pt;" class=""></span><span style="font-family: 'Times New Roman', Times, serif; font-size: 11pt;" class="">f
scripts for using Bio-Formats on the command line with bioformats_package.jar already included. Windows Operating system with 4 GB RAM. I have included in the attachment all the information.</span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><br class="">
</span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif; font-size: 11pt;" class="">I
am unable to open the converted image in any other software as well. </span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><br class="">
</span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><span style="font-size: 11pt; font-family: 'Times New Roman', Times, serif;" class="">Details
like </span><span style="font-family: 'Times New Roman', Times, serif; font-size: 11pt; text-align: justify;" class="">width, height, number of channels, Z slices, and timepoints are attached in the screenshots.</span></span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><span style="font-family: 'Times New Roman', Times, serif; font-size: 11pt; text-align: justify;" class=""><br class="">
</span></span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><span style="font-family: 'Times New Roman', Times, serif; font-size: 11pt; text-align: justify;" class="">Please
look into it and advise accordingly.</span></span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><span style="font-family: 'Times New Roman', Times, serif; font-size: 11pt; text-align: justify;" class=""><br class="">
</span></span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><span style="font-family: 'Times New Roman', Times, serif; font-size: 11pt; text-align: justify;" class="">Warm
Regards,</span></span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><span style="font-family: 'Times New Roman', Times, serif; font-size: 11pt; text-align: justify;" class="">Hitesha</span></span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><br class="">
</span></span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Helvetica, sans-serif; background-color: rgb(254, 254, 254); font-size: 11pt; text-align: center;" class=""><span style="font-family: 'Times New Roman', Times, serif;" class=""><br class="">
</span></span></div>
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<span id="cid:67B02EF5-B121-4839-9EC3-5BF64E794D0B@Home"><windowsversion.PNG></span><span id="cid:41DE627C-5D5E-4064-A432-5778DC551FAD@Home"><detailsof image2.PNG></span><span id="cid:F3C4EEDE-440F-46AA-88A6-E8C1063DAD17@Home"><detailsofimage1.PNG></span><span id="cid:3CDC2BC9-F916-4BFF-ACFA-4A96B1C5B90F@Home"><detailsofimage3.PNG></span><span id="cid:E9A287F9-17BA-47D8-B9EF-3BAA90BFFF1B@Home"><errorinopeningfile_4GBsize.PNG></span><span id="cid:A3CB6013-F08E-4F17-9FD4-40323B362951@Home"><bftoolsdetails
(2).PNG></span><span id="cid:777FAE33-2DF4-4F48-B5D9-BF88A5E34713@Home"><bftoolsdetails.PNG></span><span id="cid:193B3F65-BD8C-4ECA-B473-30208F0F6C4B@Home"><erroropeningTIFFfile.PNG></span><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: 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;" class="">
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