📄Batch Analysis

Integrate GAT into your workflow!

GAT can now be called from within a macro, making it possible to integrate it into your Fiji analysis workflows.

Please note that only Analyze Neurons is supported currently.

This functionality to call GAT from another macro is due to the use of script parameters within GAT for generating the interface. This enables the user to run GAT without any user interaction with dialog boxes. For this to work, you will first need to define the specific arguments for GAT within an ImageJ macro.

There are two sets of arguments that must be defined.

1. The first set of arguments are the ones you see in the interface when clicking the Analyze Neurons menu item.

2. The second set of arguments are the ones that correspond to spatial analysis, finetuning segmentation and ganglia segmentation. These are highlighted in orange below. They are

Arguments required:

• Image Path

• Hu or pan-neuronal marker channel

• Ganglia detection (true/false)

  • Ganglia detection method

  • Ganglia channel

  • Ganglia ROI path if detection method is "Import custom ROI"

  • Cell expansion value if detection method is "Define ganglia using Hu"

• Spatial Analysis (true/false)

  • Expansion or neuron dilation value (default = 6.5 µm)

  • Save parametric image (true/false)

• Enter custom Stardist detection values

  • Probability

  • Overlap

• Contribute to GAT (true/false)

  • Path to save images and masks (optional)

• Scaling factor (default = 1).

A complete example of an ImageJ macro is provided below. Please note that 'true' or 'false' will need to be passed as a string and not as a boolean.

You can also download this as a macro by clicking here.

/***Calling Analyze_Neurons from another macro
 * will need to be called as run(" Analyse Neurons"); with a space at start of the command. This will bring up the dialog box for entering values
 * 
 * If arguments need to specified, they can be specified in a variable args and called as run(" Analyse Neurons",args);
 * 
 * boolean needs to be passed as a string, i.e., true should be "true"
 * The dialogboxes won't work when calling from another macro, so will need to manually specify values if you want to specify custom
 * probability and overlap values, and if you want to do spatial analysis. Otherwise, defaults end up being used
 * Defaults are:
 * probability = 0.5
 * overlap = 0.3
 * For spatial analysis, if set to true, defaults are
 * label_dilation = 6.5  #micron
 * 
***/
//cannot use dialogbox when calling from macro as we use script parameters in main code; some incompatibility

//Specify values for the Dialog box when clicking "Analyze Neuron"
//The defaults are the last value you used when running the code

//Choose image to segment -> specify image path
path = "C:/GAT/Sample Images/2D_enteric_neuron_IF/181107_ms_distal_colon_GFAP_Hu_40X.tif";

///specify if image is already open: "true" or "false"
image_already_open="false";

//Channel number for Hu (pan-neuronal marker)
cell_channel=2;

//checkbox if you want to count cells per ganglia: "true" or "false". 
cell_counts_per_ganglia="true";

//Ganglia detection method. Either of ["DeepImageJ","Define ganglia using Hu","Import custom ROI"]. In this mode we are not using "Manually draw ganglia"
ganglia_detection="DeepImageJ"; 

//channel number in image for segmenting ganglia; only valid for DeepImageJ
ganglia_channel=1;

//If "Import custom ROI" is used, we need to specify path for imagej roi file containing ganglia rois
ganglia_roi_path= "";

//if "Define ganglia using Hu" is chosen, need to specify the cell expansion distance to define the ganglia. Leave as is for defaults
cell_expansion=12; //micron

// if specifying perform_spatial_analysis or finetune_detection_parameters as true, batch parameters have to be used to pass the values; otherwise defaults will be used
//perform_spatial_analysis: "true" or "false". 
perform_spatial_analysis="false";//leave as "false" if not using
//specify the label_dilation value (nearest neighbour distance) in micron; default is 6.5 micron
label_dilation=6.5;
//save_parametric_image:"true" or "false", which if true will save colour coded image with colour specifying number of nearest neighbours
save_parametric_image="true";

//finetune_detection_parameters; specify custom probability and overlap values for segmenting neurons
//if true, need to specify probability, overlap and scale (rescaling factor ) or defaults are used 
finetune_detection_parameters="false"; //"true" or "false". leave as "false" if not using
//probability value: value between 0 to 1
probability=0.5;
//overlap: value between 0 to 1
overlap=0.3;
//scaling factor. value of 1 will rescale image to match images from training dataset of the model (0.568 micron per pixel)
scale=1;
//cannot specify custom roi for hu yet

//if you want to save image masks for your analysis; leave as is if not using
contribute_to_gat="false"; //"true" or "false
img_masks_path="NA"; //directory location to save image and masks"


//batch parameters can be "NA" or specify values corresponding to spatial analysis, finetune detection parameters,  contribute_to_gat and ganglia segmentation (ROI or define ganglia using Hu)
//to pass values for spatial analysis or finetune_detection parameters, they need to be specified under batch_parameters
//they will have to be passed as a string and separated by comma
//They have to be passed in the order
//ganglia_roi_path, label_dilation,save_parameteric_image,scale,probability,overlap,img_masks_path,cell_expansion
//you can pass the defaults shown above if you don't want to change anything 
batch_parameters = ganglia_roi_path+","+label_dilation +","+save_parametric_image +","+scale +","+probability +","+overlap +","+img_masks_path+","+cell_expansion;
//if not using, pass "NA"
//batch_parameters="NA";

//all arguments together in one long string. Note that strings with spaces will need  to be enclosed in brackets, such as path, ganglia_detection and batch_parameters
args = "path=["+path+"] image_already_open=false cell_channel="+cell_channel+" cell_counts_per_ganglia="+cell_counts_per_ganglia+" ganglia_detection=["+ganglia_detection+"] ganglia_channel="+ganglia_channel+" perform_spatial_analysis="+perform_spatial_analysis+" finetune_detection_parameters="+finetune_detection_parameters+" contribute_to_gat="+contribute_to_gat+" batch_parameters=["+batch_parameters+"]";

//call Analyse Neurons -> Note that the command has a space at the start
run(" Analyse Neurons",args);