Visualize

OptiNiSt visualizes the analysis results by plotly.

Adding a Display Box

Click the “+” button to create a display box.

To add another display box , click the “+” button. You can add new boxes to the next row or the next column.

Selecting an Item to Show

Pull down of the Select Item shows the available item to show. Select one of these items.

Items are separated by the data / algorithm nodes used to create them.

Checking Movies

You may want to check some frames of the multi-page tiff files. Visualize page offers the way to check.

After creating a plot box by clicking on + mark, Select the image using the Select Item dropdown list.

You can select the range of the frames using the Start/End Index in the left sidebar. Input the first and last frame numbers, then click the LOAD button.

Click on the PLAY button within the plotting box to play the loaded movie. The number indicated on the right of PAUSE button is the frame interval in milliseconds.

Note

Lazy-loading of movies for CaImAn has not yet been implemented, which may lead to increased loading times for large datasets.

Customizing Visualization Parameters

Select one of the display boxes by clicking inside of the box. The selected box will be highlighted with a blue outline.

The left sidebar shows the parameters available for the selected box.

ROI and timecourses

In order to visualise the fluorescence time series of ROI, two visualise boxes must be created and linked.

First create one box with the imaging data. Select the imaging data file (e.g. .tiff) from the Select Item drop down menu.

Then select the ROI (e.g. cell_roi). Both Suite2P and CaImAn include the process to remove the extracted ROIs that do not meet the criteria. You can visualise ROI that have been removed by selecting non_cell_roi.

The plotting box (#0) shows the background image and detected cells. In OptiNiSt, a cell ID is given to all the ROIs and will be used for visualisation. Hover over an ROI to see the cell ID.

In another plotting box (e.g. #1), select fluorescence from the Select Item pulldown. Link two boxes by setting Link to box (#) in the fluorescence box to match the # of the ROI box (Number # of the box is on the left upper side). By clicking on the ROI of a cell, you can visualize the corresponding fluorescence time course in the fluorescence box.

Once linked, TimeSeries plots will synchronize the ROI and time courses between boxes. The color of ROI and corresponding time course is matched. Clicking on the cell automatically adds the fluorescence time course of the clicked cell.

You can select multiple ROI at once by turning on the drag select function on the right in the plotting box of ROI. It enables selecting all the ROI within the rectangular area you define.

Switch Time Course Plot Units

By default, timecourse plot’s x axis is frame number. You can switch to time unit by clicking range unit in left side bar. If you change unit to time, plot’s x axis is changed to time(sec).

The time is calculated from imaging_plane.imaging_rate, in NWB settings.

Important

The NWB settings parameter imaging_rate is also used as parameter for frame rate like fs in suite2p. So, confirm your imaging_rate is set correctly before running workflow.

Editing ROI

To the edit roi, open a plotting box and select a background image such as meanImg from the Select Item pulldowns. In the same plotting box, select cell_roi from the Select Roi pull-downs. The plotting box (#0) will show the background image and detected cells. Click Edit ROI to bring up the editing options.

Select from the three edit ROI options: Add ROI, Delete ROI, Merge ROI.

Click the Add ROI button then drag-drop and resize the white circle to change the new ROI position and size. Click OK or Cancel button to Add or not.

Click Merge ROI (when you combine 2 or more ROI cells) or Delete ROI or Cancel button to Merge or Delete or not.

To keep changes and see them in the analysis you must Commit Edit.

NWB file is overwritten with the ROI edit information.

Note

ROI edit information in NWB file

• common

  • Edited ROI ids are recorded in processing/optinist section

• specific

  • merge

    • iscell data of ROIs to be merged changes to False

    • ROI after merge are added with new ID

  • delete

    • iscell data of deleted ROI changes to False.

Saving Plots

You can save plots in SVG, PNG, JPEG, or WEBP format.

Please select the format and set the file name on the the SaveFig section in left panel. Then click the camera mark in the plotting box.

SVG format saves the plot as a vector-based graphical format which may be convenient when you need high-resolution figures.