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abria / TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images
http://abria.github.io/TeraStitcher/
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No voxel dimension information available on the meta information of "TIFF (tiled, 3D)" image generated by TeraStitcher/TeraConverter #46

Open rmd13 opened 5 years ago

rmd13 commented 5 years ago

I'm using TeraStitcher and in the final output step, I use TeraConverter instead to do the generation of final tiff image.

teraconverter.exe -s="D:\QMDownload\8\single_neuron_40X_3_extraxt\iHireMaster_1\xml_import.xml" -d="D:\QMDownload\8\single_neuron_40X_3_extraxt\iHireMaster_1\output" --sfmt="TIFF (unstitched, 3D)" --dfmt="TIFF (tiled, 3D)"

The final single tiff file I got is a z-stack of RGB channel. When I open the file in Imaris, I found that the voxel size x,y,z all are 1, but I have record the actual size in .xml file:

<?xml version="1.0" encoding="UTF-8" ?> <!DOCTYPE TeraStitcher SYSTEM "TeraStitcher.DTD">

So does the voxel size information are supposed to be not recorded in the tiff file? Thanks.
rmd13 commented 5 years ago

Below is the xml file:


<?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE TeraStitcher SYSTEM "TeraStitcher.DTD">
<TeraStitcher volume_format="TiledXY|2Dseries" input_plugin="tiff2D">
    <stacks_dir value="D:\QMDownload\8\single_neuron_40X_3_extraxt\iHireMaster_1\" />
    <ref_sys ref1="1" ref2="2" ref3="3" />
    <voxel_dims V="0.1397" H="0.1397" D="-1" />
    <origin V="0" H="0" D="0" />
    <mechanical_displacements V="261.2366" H="317" />
    <dimensions stack_rows="1" stack_columns="2" stack_slices="30" />
    <STACKS>
        <Stack N_CHANS="3" N_BYTESxCHAN="1" ROW="0" COL="0" ABS_V="0" ABS_H="0" ABS_D="0" STITCHABLE="no" DIR_NAME="[1,1]" Z_RANGES="[0,30)" IMG_REGEX="">
            <NORTH_displacements />
            <EAST_displacements />
            <SOUTH_displacements />
            <WEST_displacements />
        </Stack>
        <Stack N_CHANS="3" N_BYTESxCHAN="1" ROW="0" COL="1" ABS_V="0" ABS_H="2269.1687" ABS_D="0" STITCHABLE="no" DIR_NAME="[1,2]" Z_RANGES="[0,30)" IMG_REGEX="">
            <NORTH_displacements />
            <EAST_displacements />
            <SOUTH_displacements />
            <WEST_displacements />
        </Stack>
    </STACKS>
iannellog commented 5 years ago

Il giorno mer 6 feb 2019 alle ore 08:22 rmd06 notifications@github.com ha scritto:

I'm using TeraStitcher and in the final output step, I use TeraConverter instead to do the generation of final tiff image.

teraconverter.exe -s="D:\QMDownload\8\single_neuron_40X_3_extraxt\iHireMaster_1\xml_import.xml" -d="D:\QMDownload\8\single_neuron_40X_3_extraxt\iHireMaster_1\output" --sfmt="TIFF (unstitched, 3D)" --dfmt="TIFF (tiled, 3D)"

The final single tiff file I got is a z-stack of RGB channel. When I open the file in Imaris, I found that the voxel size x,y,z all are 1, but I have record the actual size in .xml file:

So does the voxel size information are supposed to be not recorded in the tiff file? Thanks.

the voxel size information is not currently recorded in the tiff file. Let me know if this informartion is important for you because I am planning a number of improvements and I could include this among the things to do.

Best.

-- Giulio

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

rmd13 commented 5 years ago

This information is important but I can add it to tiff in post-processing steps. Thanks.