3D View multi tile z-stack file czi cofocal

[r100gs]

Hello together,

we have an Zeiss LSM 710 confocal with the possibility to make multi tile z-stacks, but stitching is not very well.

So I tried Bitplane Imaris Software which works quite well. 

Now I am searching about a free software which can handle my files.

My questions are:

Can icy handle czi or lsm files with arround 4GB?

Can I stitch such files with icy?

Can I generate a 3d-View with such files?

Best regards,
Stefan

[Stephane]

Hi Stefan,

Icy can open CZI or LSM file but you need to allocate enough memory as Icy will maintain the full image in memory (so you need a 64 bit java with at least 8 GB allocated for Icy here, maybe more if image data is compressed).

Also Icy should automatically stitch tiles together for multi tiles image but this is very basic stitching (just connecting tiles together, no overlap).

As long you have a 3D stack you can see it in 3D in Icy through the 3D VTK view (again you may need a lot of memory for that).

Best,

- Stephane

[r100gs]

Hello Stephane,

I can open the document (I gave 26GB of memory to icy), but if I press 3D-VTK I get the message: Not enough memory". Is this possible? 2D-View is fine.

[Stephane]

Hi Stefan,

I think you have enough memory, the problem is that your 3D dataset is probably over 2 GVoxel in size (which is a hard limit for VTK). Can you give me the size (X, Y, Z and number of channel) of your dataset ?

Best,

- Stephane

[r100gs]

The size is 2486 x 1861 x 324

[Stephane]

Which is 1 498 968 504 voxels and so below the 2^31 limit, as long you have enough memory and only a single channel in your image then it should open (even if it's slow). How memory you allocated for Icy (and how much your have on your computer) ?

Best,

- Stephane