BD Cellismo™ Data Visualization Tool
Frequently Asked Questions
- Does the BD Cellismo™ Data Visualization Tool accept Seurat objects as input? Can I import a .RDS file into the BD Cellismo™ Tool? A : Not currently, but we will assess the feasibility of this for a future release. You can export Cell Annotation / Metadata from the BD Cellismo™ Tool and load that into Seurat for the same cells.
- Can I convert RDS to H5MU for loading into the BD Cellismo™ Tool? A : There are several tools for converting between Seurat and Scanpy/Muon format, but we have not assessed their capability at this time.
- Which version of the BD Rhapsody™ Sequence Analysis Pipeline should be used to make sure we output .cellismo files? A : Sequence Analysis Pipeline version 2.3 and above will have a .CELLISMO output file. For prior pipeline 2.x versions, use the .H5MU or .H5AD file.
- Does cell type annotation on the BD Cellismo™ Tool use the “cell type experimental” information from the pipeline or can I create my own annotations? A : The cell type experimental annotation for PMBC populations is automatically included in the .CELLISMO file, but users can also create their own cell annotations, either by manually selecting cells, with clustering algorithms, or with CellTypist.
- How can I remove groups/samples/annotations from the data set? A : The Quality Control page contains tools for removing cells based on metrics or annotations. Or if you don’t want to remove the cells, the Cell Annotation page contains tools for editing or removing annotation categories.
- Can I copy annotations? A : The “Edit Cell Annotation” tool has a duplicate button.
- How do I remove a cluster from the heatmap? A :Within the heatmap options, click the Select Annotation Categories button to hide or reorder specific categories.
- How can I get rid of multiplet and undetermined categories from my graphs and analysis? A: The Quality Control tool – Remove Categorical Cells.
- Can I sort/arrange categories in my graphs? A : Rearrange or sort categories in the Edit Cell Annotation tool
- How do I resize my graphs? A: In the interface, graphs will usually take as much space as they can. The Export button on the toolbar has the ability to specify pixel width and height for images saved to your computer.
- Where can I find a summary of what exactly has been done with the data upon initial import? A : On the Start Project page, press the Start Project Details button to get the summary.
- Where can I find an option to display cell counts for annotations categories in a graph? A : Cell counts for each category can be seen in the category legend of scatter type plots. They are also in the Edit Cell Annotation tool.
- How can I import bioproduct lists from .csv files to add to the bioproduct sets? A: Copy your list from the CSV and paste it into the entry box that says “Search or paste list.” Symbols can be delimited by spaces, commas or newlines.
- Where I can view what is included in each bioproduct set created? A: In the Utility Tools page – Bioproduct Sets tool.
- How can I integrate data sets from different experiments or from different cartridge lanes? Does the BD Cellismo™ Tool have a batch correction feature to allow for better integration of data across runs? A : When loading more than one dataset or pipeline result into a BD Cellismo™ Tool project, a new Cell Annotation called “Original Sample” will be created. If batch correction is required, that must first be done outside of the BD Cellismo™ tool. We will assess the feasibility of including batch correction for a future release.
- When I combine data from multiple lanes of the cartridge, is there a way to identify cells from each lane in the UMAP plots? A: When loading more than one dataset or pipeline result into a BD Cellismo™ Tool project, a new Cell Annotation called “Original Sample” will be created, and all cells will have an entry of the original file they came from.
- Do I have to have to unzip the single SMK files as MEX first before importing them into the BD Cellismo™ Tool or can I import a zipped file? A: When loading a MEX file to start a project, the file should remain zipped. For datasets that include sample multiplexing (SMK), the .CELLISMO file will already contain sample multiplexing metadata for all cells of the pipeline run so there should not be a need to load individual SMK MEX files.
- What’s the difference between creating a new category for an annotation vs a completely new annotation? A: Cell Annotations are metadata about each cell. It could be numerical (like “Percent mitochondrial”) or categorical (like “Cell Type”). Categorical Cell Annotations have one or more categories, e.g., “B cell”, “T Cell.” Within a specific categorical cell annotation, if a cell is not within any of the existing categories, it will be labels as “<unassigned>”
- When working with the differential expression page, is it possible to compare multiple comparison categories vs a reference category without creating a new annotation? A: You can select multiple comparison categories to compare against a single reference category. There is a special reference category called “rest”—meaning all other cells that are not in that comparison category. In the differential expression results, use the dropdown in the top left to select from the multiple comparison categories.
- How can I label key genes that I wish to draw attention to in the volcano plot? A: Click on the specific dot in the volcano plot and the name of the gene will be displayed and can also be exported in your graph in the gallery.
- How can you identify multiple samples multiplexed in one lane (with SMK) versus identifying samples from different lanes? A: When starting a project with .CELLISMO or .H5MU file(s), sample multiplexing results will be automatically included as a cell annotations called “Sample_Tag” and “Sample_Tag_Name.” When loading more than one pipeline result into a BD Cellismo™ Tool project, a cell annotation called “Original Sample” is automatically included.
- Can AbSeq data be analyzed alone without WTA data? A: Yes.
- Can I do the following in the BD Cellismo™ Tool?
- Pathway enrichment—Not at this time
- Transcription factor analysis—Not at this time
- Trajectory analysis—Not at this time, we have noted this as a feature request
- VDJ or ATAC analysis—Not at this time. We are working on these.
- In order to continue my analysis in either R or Python, can I have an annotated file exported out at the end of my analysis from the BD Cellismo™ Tool? A: Use the “Export Cell Annotations” tool to create a CSV.
- How can I export data to share with collaborators? A: Export a .CELLISMO-PROJECT file from the “Import/Export” tab on the Home page.
- In the Quality Control section, do you have any recommendation on what filters I should use? A: Filters and thresholds are very much dependent on cell types and sample of origin. Using a threshold for high percent mitochondria is common to remove cells that may be dead or dying.
- What is the maximum number of cells that can be handled by the BD Cellismo™ Tool? Or what is the largest number of cells that we have tested internally? A: This depends on the amount of memory available on the computer that is running the BD Cellismo™ Tool. Current guidelines are:
8 GB RAM minimum
16 GB RAM for 200,000 cells
64 GB RAM for 1M cells
Internally, we have analyzed a dataset of 1.2 million cells.
- I want to identify subclusters of cells and see gene expression levels in only those subclusters. How can I do this? For subpopulations, I want to increase the resolution and add clusters and reflect that in the original UMAP. How can I do this? A: For now, you can create a separate project and remove cells that are not of interest. Then, new dimensionality reduction coordinates and clustering results can be generated. We will look to improve handling of subsets of cells in future releases.
- While loading data, does the BD Cellismo™ Tool point out replicates or similar files uploaded by mistake? A: No, we do not attempt to identify file level duplicate mistakes. But you should be able to notice issues like that with the “Original Sample” cell annotation.
- I know that VDJ data analysis is currently not supported. However, I had some BCR runs that I had uploaded. The cell annotation seems to have information regarding all the B cell subtypes. How is this happening? A: The BD Cellismo™ Tool does not currently include VDJ specific tools but the BD Rhapsody™ Sequence Analysis Pipeline generates a rich set of TCR and BCR metadata and those are included as cell annotations when loading data from a pipeline .CELLISMO or .H5MU file.
- Can I label whole clusters on a UMAP plot (i.e., labels overlaid onto UMAP like a publication figure might have)? A: No, we do not currently enable large labels on top of scatter plots. We will assess the feasibility of this for a future release.
- If I accidentally deleted a graph from my gallery, is there any way to recover it? A: No, but if you remember what it was, it should be fast to regenerate it!
- In the quality control, once cells are excluded, is there any way to redo it or do I have to start the analysis from scratch? A: Once cells are deleted in Quality Control tools, they currently cannot be recovered and it would be best to start again from the original data. We will assess the feasibility of recovering cells for a future release.
For Research Use Only. Not for use in diagnostic or therapeutic procedures.
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