Unable to open files in MIB

I have a data file saved as an amira with all of the mitochondria of the dataset segmented, I just want to include the ones that fall within certain cell boundaries but the file won’t open on MIB, even though it’s only 800k kb in size. When I try to upload the EM images (to see the cell boundaries) the file is too large and I can’t open a model with it. How would I go about this in mib?

Hi Hannah,
Which version of MIB do you use?

Could you please clarify the following?

I have a data file saved as an amira with all of the mitochondria of the dataset segmented

How that amira-file was generated? Have you saved the model from the Menu->Models->Save model as->Amira Mesh binary?

I just want to include the ones that fall within certain cell boundaries but the file won’t open on MIB

Sorry it is not totally clear. You segmented mitochondria in a cell or few cells, saved it to disk as Amira and can’t open back? Have you tried to save the model in the MIB *.model format and load it back?

When I try to upload the EM images (to see the cell boundaries) the file is too large

You can’t open original EM images because the file is too large, right? How big is the file? How much memory do you have? How you were able to segment it in the first place if you can’t open it?

In a typical segmentation workflow you need to load EM images, do segmentation, save model in MIB *.model format. Whenever needed you can additionally save the model in various formats (Amira Mesh, TIFs, HDF5, NRRD, MRC, STL…) to use with other programs.
Due to compatibility issues we always keep original segmentations in *.model format.

Best regards,
Ilya

Hi Ilya!

I use the version of MIB for windows that’s paired with matlab. I wasn’t the one that created the amira file so I’m not sure how it was generated but I can open it in amira still, we’re pretty certain that they chopped the images and then joined them again.
Can we import multiple masks into MIB? The images of the cell boundaries is also only about 700k KB. I use ‘.model’ myself, I’m just trying to access an old dataset.

I wasn’t the one that created the amira file so I’m not sure how it was generated but I can open it in amira still

If you can open them in Amira, you should also be able to open those in MIB. Sometimes there are may be issues due to some specific metadata in the header section of amira-mesh file.
Could you please copy here the error message which you see when trying to open the model in AM format? It should be displayed with red text in matlab command window.

Another possibility is the different size of the model file, for example your EM dataset is 1024x1024x512 pixels and the model size does not match these dimensions. This may be the case if the dataset was chopped before.
Have the model files were joined back or they are still as the chopped blocks?

If the model files are chopped you need to import them using Menu->File->Chopped images->Import dialog.
Open the original dataset and import the model files:
http://mib.helsinki.fi/help/main2/ug_gui_menu_file_chop.html

Can we import multiple masks into MIB?

Do you mean a case when the full mask is chopped in number of blocks? You can import this chopped blocks and fuse them to the open dataset individually (Menu->File->Chopped images->Import->Fuse into exising). But it will only work for images and model files; the mask files do not have bounding box information and because of that the can’t be fused into the open dataset but can be imported all together.

Hi Ilya,

It doesn’t give me an error message in matlab it just doesn’t load (we’ve left it for half an hour), I have to force quit the program from ‘end process tree’. I’ve tried it on a couple of computers and it does the same thing each time. The model files were
joined back. If a have a mask open and load another mask will it add to the first mask or replace it?

Thanks,

Hannah

Could you send me that file? I can take a look.
Ilya

I appreciate the offer but the file is from OHSU so it’s confidential and I’m not allowed to share the file.

Thanks,

Hannah