XuvTools is developed in a cooperative effort from:
  • Chair of Pattern Recognition and Image Processing [www]
  • Friedrich Miescher Institute for Biomedical Research [www]
  • Center for Biological Systems Analysis [www]
 

Frequently Asked Questions

Input / Output File Support

What input file formats are supported?

XuvTools 1.8.0 can read many input formats. It makes use of several different file reader libraries:

  • Dmitry Fedorov's BioImage: PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III, JPEG, PNG, BMP, IBW, OME and RAW.
  • OME Bio-Formats: 1SC, 2FL, AFM, AL3D, ARF, AVI, BMP, C01, CFG, CXD, DICOM, DM2, DM3, DTI, FDF, FFF, FITS, FLEX, FLI, GEL, GIF, HDR, HIS, HTML, IDS, IMG, IMS, IPL, IPM, IPW, JP2, JPG, JPK, LABELS, LIF, LIFF, LIM, MDB, MNC, MNG, MOV, MRC, MRW, NAF, ND, ND2, OBSEP, OIF, OME, PAR, PCX, PDS, PGM, PICT, PNG, PR3, PS, PSD, R3D, RAW, SCN, SDT, SEQ, SLD, SM3, STP, SVS, SXM, TGA, TIF, TIFF, TOP, TXT, VWS, WAT, XML, XQF, XV, ZVI

Computer Requirements

How much RAM do I need?

You need as much RAM as you can get! From 8 to 16 GB are ok, 32 GB are good, 128 GB are better! You need roughly twice as much RAM as your dataset is large, i.e. a 6 GB LSM stitching requires 12 GB of RAM!

Image Acquisition

Do I need overlap between image stacks?

You do not need overlap between the stacks if you do manual stitching, stitching with file coordinates, or grid stitching. These modes are called “hard stitching”, because no automatic fine-tuning is applied. Stacks will be placed based on the coordinates they have been assigned manually, from the stage, or from the grid. For automatic stitching with fine-tuning on the other hand, neighbouring images need to have at least 5% to 10% overlap (more is always ok!). Very important: in the overlapping region, there needs to be some structure (neuron, cells, beads, whatever). No matter what, any structure is good! Plain background is useless!

Do I need to do grid-like acquisition?

You do not have to stick to a grid when imaging. Feel free to use the joystick, and follow your structure with the table. But remember to keep 5% - 10% overlap between neighbouring image stacks!

What microscope settings should be used?

Always use zoom=1.0 (no zoom), else you can get border artifacts (barrel distortions or similar) that make stitching almost impossible!

Are multiple channels supported?

Yes, multiple channels are supported. Actually, multiple channels are good! The more channels you have, the more likely you will get good stitching results.

Are brightfield collected channels helpful?

Brightfield is not likely to help for the stitching, since brightfield has a plane of focus, which is a fundamental difference to confocal stacks.

What bit-depths are supported?

All bit depths are supported by XuvTools. You can use 8, 12, or 16 bit (or more if you have!). A higher bit depth is good, and can help improve stitching quality.

Do all stacks need to be the same magnification?

No! You can do stacks with different objectives and different binnings if you like. I.e. you can use a 10x objective for an overview, and then use a 63x objective to image details inside your overview! XuvTools will scale all stacks to the finest resolution available.

faq.txt · Last modified: 2014/04/09 10:41 by niko
Contact: admin(a)xuvtools.org