Converting HDF5 Imaris file using TeraConverter

[katom16]

Hello, I am trying to convert my .ims files which I believe as a supported format for TeraConverter, but errors show up as: [ERROR: in VirtualVolume::instance(): Unsupported format "HDF5 (Imaris IMS)" for path....

If you have any suggestions, it would really helpful.

Thank you for your support in advance,

[iannellog]

Actually TeraConverter does not accept as input an .ims file (it is not difficult to add, but I did not do that so far). However you can convert an .ims file pretending it is an unstitched image consisting of just one tile.

The procedure is:

• put the ims file to be converted in a folder 'path'

• modify the attached xml file as follows: 1) at row 4 set the attribute 'value' to 'path 2) at row 12 set the attribute IMG_REGEX to the name of the ims file 3) at row 12 set the correct number of channel and the bytes per channel 4) optionally set the voxel size to the right values (row 6), otherwise a size 1 x 1 x 1 um is used, which should not be relevant if the output format is a series of tiffs 5) set the resolution and time point you want to convert (if there is only one resolution and timepoint do nothing)

• use the GUI of TeraStitcher to normally import the dataset and save the "stitched" image in the output format you choose (the quotes mean that of course it is not an actual stitching, but only a conversion) or launch the command

teraconverter --sfmt="TIFF (unstitched, 3D)" -s=complete path of the xml file --dfmt=format of the converted image -d=folder of the converted image --imin_plugin=IMS_HDF5

Let me know if you have problems. Best.

-- Giulio

2018-01-29 9:19 GMT+01:00 katom16 notifications@github.com:

Hello, I am trying to convert my .ims files which I believe as a supported format for TeraConverter, but errors show up as: [ERROR: in VirtualVolume::instance(): Unsupported format "HDF5 (Imaris IMS)" for path....

If you have any suggestions, it would really helpful.

Thank you for your support in advance,

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/abria/TeraStitcher/issues/25, or mute the thread https://github.com/notifications/unsubscribe-auth/AIdv1tmaFprjmnyZFJDTK4HcSvduZgVGks5tPX74gaJpZM4RwNm- .

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Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

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[katom16]

Thank you for your reply. I am grad to hear there is still a way to convert imaris files.

However, I couldn't find any xml file in my TeraStitcher folder... Where should I look for the file?

Thank you.

[rmd13]

Hi, iannellog.

I'm tring to convert a ims file with XYZCT dimensions to tiff files either in XYZ per file and _C_T /_T_C in filename series , or XYC per file and _Z_T/_T_Z in filename series , or in XYT per file and _Z_C/_C_Z in filename series. Or to Tif files with XYZT per file and _C in file name series, etc. Can this programme do this? Thanks.

[rmd13]

Hi, katom16 You can save the ims file as tiff format or other common format, so they can be opened by other programme that does not read ims files.

[iannellog]

Is this a question for me? Please clarify. In any case I already explained in this thread how to do this (see my answer on Jan 30, 2018). If you need the example xml file you have to sent me your personal email since GitHub does not accept attachments. Best.

-- Giulio Il giorno lun 27 ago 2018 alle ore 15:40 rmd06 notifications@github.com ha scritto:

Hi, katom16 You can save the ims file as tiff format or other common format, so they can be opened by other programme that does not read ims files.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

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Giulio Iannello Preside della Facolta' Dipartimentale di Ingegneria Universita' Campus Bio-Medico di Roma v. Alvaro del Portillo, 21 00128 Roma, Italy

Tel: +39-06-22541-9602 E-mail: g.iannello@unicampus.it Fax: +39-06-22541-9609 URL: https://scholar.google.it/citations?user=L-UJxIgAAAAJ

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[dany-fu]

Hi @iannellog I am having the same issue. Is the procedure to convert .ims files still the same as the process you described on 1/30/2018?

[k1moradi]

Hi, @iannellog I'm trying to convert ims to tiff but I cannot find the XML file you mentioned earlier. Could you please share it here?