Gatan DM4 stiching failed

[bpavie]

I tried to Stiched Gatan DM4 files but it failes with the following error:

Error unable to find file: I:\30nm\montage 2, 3.7K\New folder\TEST\Prefix_3VBSED_stack_01_slice_0000.dm4. Skipping timeslice: 0

But this file exist and is actually open later on via the bioformat importer.

The stitching is working with the plugin Grid/Collection stitching

[mmajurski]

Can you open the image(s) in question using stock ImageJ?

Given some quick googling it appears that BioFormats will read some .dm4 files and that stock ImageJ does not have a reader for that type of file.

Since MIST uses the stock ImageJ image reader it is unable to read images that ImageJ itself cannot read.

Unfortunately it looks like you will have to convert the images into a format like .tif in order to use MIST. If BioFormats can read the images (I believe that Grid/Collection stitching utilizes the BioFormats plugin) then you should be able to use BioFormats to convert them to .tif and then stitch. Its kind of a pain, but it looks like its the only way to do it currently.

Thanks,
Michael Majurski

[mmajurski]

What type of image is the Gatan DM4 file? Does the file "I:\30nm\montage 2, 3.7K\New folder\TEST\Prefix_3VBSED_stack_01_slice_0000.dm4" contain a single 2D image? Or is it multi-planer, multi-channel, or multi-time-point within the same .dm4 file?

BioFormats can handle very complex multi dimensional images that MIST cannot. However, this comes at the cost of speed. BioFormats is signifigantly slower than the stock ImageJ file reader.

I have an update almost ready that enables using BioFormats to read one 2D image per file. Without major changes to how MIST organizes the images it cannot handle loading multi-dimensional images from a single file.

If you don't mind giving me a copy of the images you are trying to stitch I would be happy to see if I can coerce MIST into handling them?

Thanks,
Michael Majurski