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ClearAnatomics / ClearMap

ClearMap 2 with WobblyStitcher, TubeMap and CellMap
https://clearanatomics.github.io/ClearMapDocumentation/
GNU General Public License v3.0
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how to view result.0.mhd file in imageJ? #27

Closed ywang219 closed 4 years ago

ywang219 commented 4 years ago

Hi, after alignment, I opened the result.0.mhd file which appears as following: I also tried to drag it to imageJ which does the same. What is the problem here? Thank you!

ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = True CompressedDataSize = 787716 TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = 0 0 0 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 1 1 1 DimSize = 351 416 7 ElementType = MET_SHORT ElementDataFile = result.0.zraw

SaibotMagd commented 4 years ago

ImageJ got 3 very different versions (ImageJ1, ImageJ2 and Fiji) and a lot of plugins. To load a mhd file you need a particular plugin. But I don't know the name. The easier way will be to download Fiji because it consists a lot of plugins you will need to work with Clearmap, beside the mhd-file plugin. You can download it here for example:

https://imagej.net/Fiji/Downloads

PS: an alternative way to read the files is to convert them to tif-files. This is possible if you use this command:

  io.convert_files(ws.filename('resampled_to_auto', extension='npy'), extension='tif',
                 processes=4, verbose=True);

If you do that with the "stitched.npy" file you will be able to load very large files in imageJ with the "visual stack" function (File->Import->Bioformats). So you can load files with hundreds of GB even on a somewhat poor pc. ;)