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Add section about hdf5 in the headless mode doc. #142

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Oct 16, 2020
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Add section about hdf5 in the headless mode doc. #142

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9 changes: 9 additions & 0 deletions documentation/basics/headless.md
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Expand Up @@ -53,6 +53,15 @@ CPU and RAM resources can be controlled with environment variables or a config f

[controlling resources]: {{site.baseurl}}/documentation/basics/installation#controlling-cpu-and-ram-resources

### Using hdf5 for memory efficiency

We recommend to use hdf5 for input and output over, for example, TIF stacks. Indeed, TIF stacks cannot be written/read block-wise, hence the whole data has to be loaded and kept in memory. This can lead to excessive memory usage and slowness.

In order to convert your TIF slices into hdf5 datasets, you can check the dedicated [Fiji Plugin][fiji_plugin].

[fiji_plugin]: {{site.baseurl}}/documentation/fiji_export/plugin


### Using stack input

If you are dealing with 3D data in the form of an image sequence (e.g. a tiff stack),
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