I would like to use elephant for nuclei tracking in klb files, is there any way possible to achieve that, or i should change the format?
A quick look shows:
Which leads to:
" Opening a Dataset
To use the BigDataViewer we need some example dataset to browse. There are various options:
Multi-view data converted to XML/HDF5
A special purpose of BigDataViewer is to visualise multi-view light sheet microscopy datasets. Our custom XML/HDF5 is a special purpose hierarchical data format that optimises access to any part of large-multi view datasets using ImgLib2. You can download a small dataset from here, comprising two views and three time-points. This is an excerpt of a 6 angle 715 time-point sequence of drosophila melanogaster embryonal development, imaged with a Zeiss Lightsheet Z.1. Download both the XML and the HDF5 file and place them somewhere next to each other.
Alternatively, you can create a dataset by exporting your own data as described below.
To start BigDataViewer, select Plugins › BigDataViewer › Open XML/HDF5 from the Fiji menu. This brings up a file open dialog. Open the XML file of your test dataset.
Standard microscopy data
The BigDataViewer can be used to visualise and navigate any image that can be opened in Fiji. Since Fiji relies of LOCI Bioformats library that means essentially all know microscopy file formats.
For example, open the sample image File › Open Samples › Mitosis (26MB, 5D stack) from the Fiji menu. Subsequently select Plugins › BigDataViewer › Open Current Image which will launch the BigDataViewer with the sample image, for navigation by arbitrary re-slicing.
Imaris (Bitplane) uses a hierarchical data format (similar to BigDataViewer’s XML/HDF5 format). In order to open Imaris .ims files select Plugins › BigDataViewer › Open Imaris (experimental) from the Fiji menu. Please note, that support for the Imaris format is still experimental."
Hello, Giannis Liaskas and MicroscopyRA. As MicroscopyRA mentioned, ELEPHANT is using the BigDataViewer format (
To use ELEPHANT, you need to convert your data to the BigDataViewer format.
The easiest way would be loading your data on Fiji and converting it to the BigDataViewer format using [Plugins › BigDataViewer › Export Current Image as XML/HDF5].
I found that the latest version of Bio-Formats>=6.0.0 supports the KLB format (Release announcement). I have not tried it yet but you will be able to load your data on Fiji using it.