Answers.Body: <p>If you are familiar with Python, I maintain the <a href="https://github.com/whitews/FlowKit" rel="nofollow noreferrer">FlowKit library</a> that can import FlowJo 10 workspaces and export the gate statistics as a Pandas DataFrame. From there it would be trivial to convert the data to JSON or CSV.</p>
  <p>If you want to go that route, the Workspace class handles this functionality. There are tutorials to get you up to speed, the most relevant is <a href="https://flowkit.readthedocs.io/en/latest/notebooks/flowkit-tutorial-part06-workspace-class.html" rel="nofollow noreferrer">this Jupyter notebook</a> demonstrating loading a FlowJo .wsp file along with the related FCS files and extracting the gate analysis.</p>
  
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Body: <p>How does one convert &quot;flowJO&quot; flow-cytometry cell-count data into &quot;.json&quot; or relational-database-management-system compatible files?</p>
  <p>The way flow-jo exports is in wide rather than long format. It also exports everything per subject/animal/lab-rat per specific timepoints rather than aggregating. I need the aggregated files to plot groups.</p>
  <p>It's also not shaped in a &quot;primary-key&quot;, column 1, column 2, column 3, or .json (NO_SQL) format.
  Running statistical programs or databases is intractable with the export options Flowjo gives.</p>
  <p>I am looking for some way to convert it, or maybe the problem lies in flowjo. It does not support the export formats I need.
  I amk open to other flow-cytometry software that offers better integration with no-sql/sql database.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-09-02T15:14:00.187Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Tags: <database><software-recommendation><format-conversion><flow-cytometry>
Title: How does one convert "flowJO" flow-cytometry cell-count, etc, bead, etc data into .json or relational-database-management-system compatible files?
ThreadText: # How does one convert "flowJO" flow-cytometry cell-count, etc, bead, etc data into .json or relational-database-management-system compatible files?
  
  (Asked by: username_0 on 2022-09-02)
  
  How does one convert "flowJO" flow-cytometry cell-count data into ".json" or relational-database-management-system compatible files?
  
  The way flow-jo exports is in wide rather than long format. It also exports everything per subject/animal/lab-rat per specific timepoints rather than aggregating. I need the aggregated files to plot groups.
  
  It's also not shaped in a "primary-key", column 1, column 2, column 3, or .json (NO\_SQL) format.
  Running statistical programs or databases is intractable with the export options Flowjo gives.
  
  I am looking for some way to convert it, or maybe the problem lies in flowjo. It does not support the export formats I need.
  I amk open to other flow-cytometry software that offers better integration with no-sql/sql database.
  
  **Tags:** database, software-recommendation, format-conversion, flow-cytometry
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-07-25. Score: 0 | Accepted answer
  
  If you are familiar with Python, I maintain the [FlowKit library](https://github.com/whitews/FlowKit) that can import FlowJo 10 workspaces and export the gate statistics as a Pandas DataFrame. From there it would be trivial to convert the data to JSON or CSV.
  
  If you want to go that route, the Workspace class handles this functionality. There are tutorials to get you up to speed, the most relevant is [this Jupyter notebook](https://flowkit.readthedocs.io/en/latest/notebooks/flowkit-tutorial-part06-workspace-class.html) demonstrating loading a FlowJo .wsp file along with the related FCS files and extracting the gate analysis.
  
  
  ---
  
  