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Napari Plugin

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

There are two ways to do the cropping:

  • Define ROIs within napari-lattice plugin
  • Import ROIs generated elsewhere, such as Fiji ROI Manager.

Define ROIs in napari-lattice

  • Load and configure the image in the Deskew tab and you should see a green tick.
  • Run Preview to get a deskewed volume. We will use this as a reference to draw ROIs for cropping.
  • Go to the Crop tab and tick the Enabled button to activate cropping.

crop_tick

The red text at the bottom indicates that atleast one ROI must be specified.

  • Click on New Crop at the bottom of the plugin to add a Shapes layer on the left to draw ROIs. This Shapes layer will be called Napari Lattice Crop. Click here for more info on using Shapes layers and drawing shapes.
  • Click on the Napari Lattice Crop Shapes layer and the rectangular ROI tool will be selected by default.
  • Draw an ROI around the region you would like to crop. After defining the ROI, it will appear on the right. crop_ROI
  • Similarly, you can draw multiple ROIs. Each ROI will be an entry in the ROIs box. When you select one of them, the error message below will disappear.

crop_ROI

  • Once you have drawn the ROIs, select one of them, and click Preview to visualize the cropped region. The cropped image will appear as a new layer in the image layer list on the left.

crop_ROI

  • The purpose of the Crop tab is to setup the ROIs. Once you've defined all of them, you can save all of them by configuring it in the Output tab.

Import ROIs

We have added support to import ROIs from Fiji ROI Manager file. This workflow exists because the Zeiss lattice lightsheet produces a 2D maximum intensity projection at the end of the acquisition. This image can be used to select ROIs of interest in Fiji. Refer to this page for more instructons on how to generate.

MORE INSTRUCTIONS TO BE ADDED

Instructions about importing workflows to be added

Instructions on how to save files after setting up the other tabs