If the compact waveform file (CVW) is stored in the same location as the associated FCS file, when a CellView plugin node is first applied to a file a popup window will open inquiring whether you would like to extract the image files. If you reply yes, a folder will be created in the same location as the FCS file with the required structure for the images.
The Tools menu in the CellView lens viewer all contains an option for Extract TIFF files from CVW so the action can be initiated at any point in the analysis.
Image filter controls
Remove Background - a checkbox has been added that uses specified channel(s) to identify edges within the images and assume pixels within the edges are signal, and outside the edges are noise.
Clicking on the Overlay channel with Remove Background checked converts the slider on the histogram image adjustment window to a fine tuning adjustment for the sensitivity of the edge detection. Sliding left produces a more generous threshold, right a more stringent threshold.
Alternately, there is a Find Best Threshold check box that sets the threshold automatically.
There is now an Edit Region Mask the un-grays when the Find Best Threshold is off. With this selected you can control + click any channel to include it in the edge detection to create the mask.
Shift-clicking on the overlay channel will show the regions identified by the Remove Background tool. Each unique region will be shown in a different color.
Clicking next to any channel in the channel name list adds or removes colored boxes indicating the channel will be used.
An eye icon has been added to the right of the channel list that indicates which channel will be displayed in the image wall. Click to the right of a channel name to set it.
Image browser controls
If Remove Background can been checked on four additional tools will appear as check boxes
Regions - if checked shows the regions on the Wall View.
Edges - draws the edge as determined by Remove Background
Connections - shows a line representing the shortest distance between two regions in images with multiple regions. Shows nothing if there is only one region present.
Centroids - shows a + on the centroid of all regions.
Filter Sets now automatically read the filter set from the Chorus file and use it as the default selection.
There is now a check box for show image sets
Image Sets
Checking the Show Image Sets box in the Image browser opens a blank canvas that allows the user to select images from the image wall and add them to the active image set.
Image sets are initially locked. Click the lock icon to open it and begin editing an image set.
Controls have been added to lock / unlock / remove all images from / rename /create new / duplicate / delete an image set.
A camera button is included that adds the current image wall to the layout editor.
Tools to show a dot plot with all images in an image set, either around the edge or in quadrants is present that will un-gray if the 2D plot viewer has been activated.
Find Similar Images button has been added that allows the user to select collected or derived numeric parameters, rank the cells in order of similarity to the composite of cells in the image set, and select a number of cells to include in a new image set.
Create population tool has been added that makes a FlowJo hierarchy population of the current image wall, plus a population that is the NOT of the image set.
Tools menu now contains tools to:
Interact with Image sets
Add snapshots to the layout editor
Export selected populations as new files with their images. An individual population, or multiple populations from the same sample using a Boolean OR gate, or multi-selecting populations from multiple samples can all be inputs. The output will be and fcs file + a CSV file containing the mapping of the original image number to the new file. Using this tool with the Shift held down will add these outputs to the BD Research Cloud.
Make an image file gate, which creates a derived parameter and autogates in so that cells with images go into one population and cells without images go into the other.
Generate Image files report, which creates a text file with the path to all images from the selected population.
Create Bisector gate, which creates a gate separating cells above the selected cell from cells below it, and thus implicitly gating on whatever parameter the images have been sorted on.
Open Machine Learning Tools, which have now been converted from a hidden preference to a menu option.
