Question: How do I find the CytAssist instrument firmware version that generated my CytAssist image?
Answer: There are several ways to find the CytAssist instrument firmware version used to generate a CytAssist image.
If the Visium data has not been processed and you have access to the CytAssist run logs that generated the CytAssist image, you can check the run info CSV file. An example of a run info CSV file is shown below. In this example, the CytAssist instrument firmware version is 2.0.0.19.
Run Info
Run Name,Visium_HD_run1
Unique Run ID,211bb0a3-a396-4948-a0f9-b869d44194b3
Visium Slide ID,H1-3FFJ4BH
Sample A1,A1_sample
Sample D1,D1_sample
Slide Type,Visium HD, 6.5 mm
Assay Type,CytAssist-HD
Assay Completed,1
Assay Aborted,0
Assay Cancelled,0
Error Code,None
Error Description,None
Start Time,2024-02-08@12:27:28.406
End Time,2024-02-08@12:58:22.089
Run Temperature,37C
RunTime,30 min
Serial Number,PVTFMN010
Software Version,2.0.0.19
Another option is to use the program tiffer, which is included with the Space Ranger pipeline. Starting with CytAssist instrument firmware version 2.0, the instrument firmware version was included in the metadata of the CytAssist image. We can use the program tiffer to view the metadata of the CytAsisst image using a Linux command line like the following:
/path_to_spaceranger_installaion/spaceranger-x.y.z/lib/bin/tiffer <CytAssist Image>
When using the program tiffer to view the image, the firmware version is listed after “cytassistInstrumentsSoftwareVersion”. In the example below, the CytAssist image was generated from an instrument using firmware version 2.1.0.12.
$ /path_to_spaceranger_installation/spaceranger-3.1.1/lib/bin/tiffer info CytAssist_image.tif
{"format":"tiff","checksum":"9fd1b0090a45329dae2b3c97f3ee1d2f","pages":[{"width":3200,"height":3000,"colorMode":"RGBA","depth":8}],"slideSerial":"H1-K2CWNWF","captureArea":"A1","imageDescription":"{\"shape\": [1, 3000, 3200, 3]}","cytassistRunName":"Visium_HD_run1","cytassistInstrumentSerial":"CAVG10539","cytassistInstrumentSoftwareVersion":"2.1.0.12"}
If the Visium data was processed using Space Ranger 3.1.0 or later, another way to find the CytAssist instrument firmware version is to look at the web summary HTML file, under the “Sample Metadata” table. In the example below, the instrument firmware version, circled in red, is 2.0.1.6.
Last Updated: Oct. 2024