12/17/2023 0 Comments Z stack confocalYou can give the stack a new name, or keep the generic ‘Stack’. To create a stack from multiple individual images go to Image -> Stacks -> Images to Stack.Īn options window will open. You can monitor the slice number in the image information at the top left of the image window. You can also click on the left (2) and right (3) arrows to move the stack by 1 slice or click the play button (4) to run through the stack slices automatically. You can easily move through the slices in a stack using the bar at the bottom of the image.Ĭlick and drag the slider (1) to move through the stacks. The image NeuralTube.jpeg along with its individual channels and image stacks RGBStack.tif and MovieStack.tif will be used for demonstration throughout this section. More detailed informaiton on working with multiple dimmensions in imaging and stacks is covered in FIJI Intermediate. This section goes through the tools and methods for working with image stacks. You can also generate a stack yourself from related TIFF or JPEG images. When channel, Z-series or time information is recorded the images are usually opened as stacks automatically when bio-formats importer is used to open the files. Stacks can represent different channels from the same image, z-slices captured on the microscope or time series. While I think ilastik could still get you pretty far in your analysis, minus the visualization part, I can of course understand if it is too frustrating to get there.Image stacks are composed of a number of related images opened on top of each other in a single window. I’m always happy to point to other tools or make clear that some things cannot be achieved in ilastik for specific use-cases. And I also can see how it can be frustrating to use. Please also take some time to familiarize yourself with the guidelines.įor the other issues, sure, we know that ilastik can be improved (and it continuously is), nothing wrong about stating the obvious. Most of the open source image/data analysis tools are out there and you can even ask general analysis questions where other users can point you to the right direction. I would definitely encourage you to explore the forum a bit. Hello of all, thank you for jumping in and solving the youtube usage problem! This underscores the usefulness of posting in the forum (as opposed to sending emails privately). I wish the ilastik group made a major and prompt effort to install 3D reconstruction for all modes and all computers. If I had been, I would have probably purchased Imaris that has all those capabilities. Unfortunately, I am unable to pay for commercial software. I hope you realize that there is only so much time and effort that one is able to invest before giving up on the application. I have no idea what you refer to by ‘mesh’, and how it is generated. It makes life much more complicated versus making this functionality available in ilastik. I have no clue how to input the ilastik output into one of the applications you mentioned. I am not an imaging expert and don’t have the wider knowledge of what’s available in the market, like you. Its 3D functionally is either poor or crashes when one tries to apply it. I am familiar with ImageJ and use it frequently. What I mean by ‘3D reconstruction’ is the green object in the attached screen shot. Why not overcome the problem and make it available for Mac. I wish it had been much clearer 3D reconstruction is available only in the carving mode. The next logical thought is what do I need to fix, though there is nothing I can do - I wish that had obvious. There is nothing to tell me it doesn’t work until I try it and confront an error message. The ‘3D’ option appears during this workflow. I was using pixel classification workflow.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |