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Napari Plugin

Starting the plugin

The napari plugin has been redesigned in the newer version. To activate the plugin, activate the napari-lattice environment in your terminal and type napari in the console. The plugin is under Lattice Lightsheet Analysis

Activate plugin

The plugin should appear on the right side. You may have to resize the window.

llsz_plugin

The functionalities with napari-lattice have been separated out into tabs:

plugin_tabs

If its configured correctly, you should see a green tick next to the tab name, else you will see a red cross.

green_tick

To load an image, drag and drop it into napari. You can get some sample data here. We are using RBC_tiny.czi as an example here.

open_image

Info

When opening a file, if you get a pop-up asking for preferred reader with czi files, select napari-aicsimageio

Configuration

To configure any parameters, you can change the settings here:

settings

Plugin Usage

To use the specific image for processing, you will have to select it under the Image Layer(s) to Deskew box on the right. Here, we will click on RBC_tiny. As its a czi file it should read the metadata accordingly and you will see a green tick.

deskew_active

If you are loading a czi, the metadata fields should be populated automatically.

To Preview the deskewed image, click Preview and choose the appropriate channel and time.

You should see the deskewed image appear as an extra layer with the Preview suffix attached to it.

deskewed

Extra_info

If you look at the terminal after deskew, you should see the settings used and any other metadata associated with the dataset. It is handy for troubleshooting.

From version 1.0.3 onwards, we have an option to show the Deskewed image without actually deskewing it. It does not create a new image, but simply transforms the image in the canvas to a deskewed image. This can be useful for quick preview of the data.

To do this, once the plugin is initialized, click on Quick Deskew.

quick_deskew_checkbox

Once you click it, you can view the deskewed image in the napari image canvas.

quick_deskew_active

You may get the following warning: Non-orthogonal slicing is being requested, but is not fully supported. Data is displayed without applying an out-of-slice rotation or shear component.! This is absolutely fine. It just means the image won't be displayed as deskewed in 2D mode. Hence, why we enable 3D mode.

Here is an example of browsing through a timeseries

The smoothness of this interactivity will depend on the storage read/write speeds and/or network speeds. For example, if the data is stored on the network, it will be slow to browse timepoints. However, if your data is on your SSD locally, the experience will be much better.

Deconvolution is primarily enabled by pycudadecon. For this functionality, you will need the point spread function (PSF) for the corresponding channel, either simulated or experimentally derived. You can find examples here.

Important

Ensure you are using the right PSF file for each channel. The number and order of the PSF files should match the channels in the image.

After loading the image and configuring it in the Deskew tab, select the Deconvolution tab. When you click Enable, you should see a green tick appear next to the name.

decon_tab

Under processing algorithms only cuda_gpu and cpu are supported. opencl_gpu has not been implemented yet. The next step is to select the PSF files. In this example, we will use the RBC_tiny.czi file

decon_options

  • PSFs: Use the Select files to select multiple PSF files. As the dataset was acquired in the 48 channel, we use the 488.czi PSF file here.
  • Number of iterations: Try 10 if not sure and increase if needed.
  • Background: Background to subtract.
    • Automatic: median value of last Z slice will be used
    • Second Last: median value of second last Z slice will be used. This is used in case the last Z slice is incomplete if acquisition is prematurely stopped.
    • Custom: Enter a custom value

Once you are done, click Preview at the bottom, and select timepoint or channel. You should see output from pycudadecon printed to the terminal. When complete, a deconvolved image will appear as an extra image layer. Below is an example of the deskewed image without (left) and with (right) deconvolution.

decon_compare

More instructions to be added..

More instructions to be added..

More instructions to be added..