The Image Stack module allows you to focus through an image stack in real-time. Microlucida automatically keeps track of the depth (Z-axis) values while you
What are the file formats supported?
| MBF JPEG2000 (.jp2; .jpx; .jpf) | MBF Tiff (.tif; .tiff) | JPEG2000 (.jp2; .jpx; .jpf) |
| Tiff (.tif; .tiff) | Bit Map (.bmp) | JPEG (.jpg, .jpeg) |
| ZSoft (.pcx) | PNG files (.png) | TARGA files (.tga) |
| Olympus Fluoview (.tif) | Portable Image (.pgm; .pbm; .ppm) | BioRad Confocal Image (.pic) |
| FlashPix (.fpx) | Zeiss Confocal LSM (.lsm) | Zoomify (.pff) |
| DICOM (.dcm) | ANALYZE (.img) | NanoZoomer (.ndpi; .vms; .vmu) |
| Aperio SVS (.svs) |
How do I load image stacks?
The X and Y dimensions of the imported image default to the current lens.
Select the lens that was used to capture the images before loading the image stack.
If the image stack was collected on a different microscope:
Load a single image stack file that contains all the planes
Load an image stack composed of multiple files
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If you load an image for which there is no matching lens, Microlucida prompts you to create a new lens to match the image scaling. Create a new lens/Edit a lens: Parameters.
How do I view image stacks?
The top image of a stack is loaded at the current Z position of Microlucida. When the stack is loaded, the top image of the stack is displayed.
The status bar at the bottom of the screen provides information about the plane on display.
or the Image Organizer.To visualize an entire image stack in a single plane, use Image>Maximum Intensity Projection | Minimum Intensity Projection.
How do I save image stacks?
Save Image Stack automatically opens following the Acquisition>Acquire Image Stack operation.
Image Adjustment to learn how adjustments are saved.
How do I trace from image stacks?
Tracing from image stacks is similar to tracing from a single tissue section.
Microlucida keeps track of the Z-depth of your tracing by recording the Page Up and Page Down movements through the sections.
When working with multiple adjacent image stacks, there are two methods:
There is no need for the Serial Section Manager since Microlucida treats the different images of the stack like different focal depths of the same section.
Image order and nomenclature
Single file with multiple images
A multiple-image file such as a PIC or TIF file contains all of the images for one image stack.
The images are interpreted to be sequential images with the first images placed at the top of the stack and subsequent images placed at decreasing Z positions.
The first image is placed at the current Z position.
Multiple single-image files
The order in which multiple images from single-image files are loaded is determined by the order of the files in the dialog box.
We recommend using a naming convention that facilitates image ordering.
If you name a set of images image1, image2, image3, and so on, image10 is placed after image1 but before image2.
Instead, number the images as follows: image01, image02...image10, image 11... in order to maintain the correct order.
The images are loaded in the same order as the files appear in the File>Open dialog box.