faq [2010/03/10 12:01]
mario created |
faq [2010/05/25 08:41] (current)
mario added brightfield |
| | ====== Frequently Asked Questions ====== | | ====== Frequently Asked Questions ====== |
| | + | |
| | + | ==== Input / Output File Support ==== |
| | + | |
| | + | == What input file formats are supported? == |
| | + | |
| | + | XuvTools can read many input formats: BioRad 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. |
| | + | |
| | + | ==== 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? == |
| | + | |
| | + | Yes, neighbouring images should have 5% to 10% overlap for automatic stitching. For manual stitching, you do not need overlap. 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. |
| | | | |
| | | | |