Stream from folder

Streams data from a folder containing multiple image stacks, each image stack containing the XYZ data for one channel and one time-point. If your folder contains sub-folders they will be interpreted as containing different channels. Right now sub-folders are the only way to stream multi-channel data. Please raise an issue on github if you'd like to import some other data.

Supported image stack formats

- Multi-page Tiff (LZW compression is supported)
- Hdf5

Stream from info file

Loads an info file that you saved before using 'Save as info file'.

Idea behind this functionality

Especially if your data format is compressed Tiff stacks it can take quite some time to parse all the files in a folder. Once all files are parsed you can save all the extracted information into one single Info file, which is much faster to load and thus gives you much faster full access to your data.

Save as info file

Saves the currently active virtual stack as an info file. The info file contains all the information needed to re-open the current virtual stack without duplicating any pixel data. If you open a virtual stack (data stream) from a saved info file the plugin will stream the data from the original image files. This makes sense in two cases:
1) You just selected a folder using 'Stream from folder' and want to stream the same files faster the next time you start ImageJ.
2) You cropped your data stream, either using the 'Crop as new stream' function in this plugin or using the 'Crop along tracks' function in the 'Big data tracker' plugin, and want to save the cropped view without duplicating the data.
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Save as tif stacks

Saves the current stream as a sequence of multi-page Tiff files; one file per channel and time-point.

Idea behind this functionality

A sequence of tif stacks is a convenient and readily compatible format for storage and further processing. For instance you might want to deconvolve each stack or register stacks against each other using other software such as Huygens for deconvolution or elastix for registration.

Duplicate to RAM

Loads all images and copies them into RAM. Make sure that you have enough RAM before doing this. Also be prepared that this might take quite some time!

Idea behind this functionality

Some operations are very slow or not even possible at all when the data is presented as a stream (i.e. virtual stack). Thus it might be necessary to copy the whole data into RAM.

Crop as new stream

Crops the current stream based on a rectangular selection tool and shows it in a new image window.

Idea behind this functionality

First of all the browsing of cropped data will be even faster, because the software needs to load less data per z-slice. More importantly however, the cropped data might be small enough to fit into RAM (using: 'Duplicate to RAM') and thereby enable fast processing in ImageJ; or, you may want to save the cropped data to disk (using 'Save as Tiff stacks') for further processing with other software.

Report issue

Opens the github issue web-site.