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BD CellView Image Processing

Installation

  1. Please install Fiji on your computer.
  2. Restart Fiji and install the BD CellView update site (how to install an update site).
    • BD CellView
  3. Restart Fiji

Cite

When using this plugin please cite Schraivogel, D. et al. High-speed fluorescence image-enabled cell sorting. Science 375, 315-320 (2022).

Use

For detailed instructions please see the Supplemental Material in the above publication.

Folder Structure

The folder structure must be as shown below:

Available Channel Colors

Please see the Java AWT Color specifications.

Channel indices

The ICS generates multichannel TIFFs with 8 channels. You can select those channels 1-8 in the channel indices field of the Fiji Plugin. Here's an overview of different channels.

Screen Shot 2022-03-03 at 19 23 59

Table

The table must look like this (the column name of gate may be changed as this can be specified in the user interface):

id;gate;path
id0;G2M;../images/Cell_Cycle_00000000.tiff
id1;G2M;../images/Cell_Cycle_00000001.tiff
id2;G2M;../images/Cell_Cycle_00000002.tiff
id3;G1;../images/Cell_Cycle_00000003.tiff
id4;G1;../images/Cell_Cycle_00000004.tiff
id5;G1;../images/Cell_Cycle_00011082.tiff
id6;S;../images/Cell_Cycle_00013268.tiff
id7;S;../images/Cell_Cycle_00014714.tiff
id8;S;../images/Cell_Cycle_00016839.tiff
id9;NA;../images/Cell_Cycle_00017276.tiff

Quick start

  1. Open Fiji
  2. Plugins › BD CellView › Process BD CellView Images
  3. Add files... (open the table file, s.a.)
  4. Select gate (to select the table and gate)
  5. Process random image of selected gate from selected table
  6. Configure the visualisation settings (channels and min/max gray levels)
  7. When satisfied export all images using Batch process images of selected gate from all tables