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fixed option for reading multiseries lif and a long filename
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@pr4deepr
pr4deepr committed Nov 14, 2022
1 parent 4b587f1 commit 2368852
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Showing 3 changed files with 138 additions and 51 deletions.
48 changes: 35 additions & 13 deletions _Analyse Neuron (Multi-channel - No Hu).ijm
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Original file line number Diff line number Diff line change
Expand Up @@ -146,16 +146,34 @@ if(image_already_open==true)
else
{
if(endsWith(path, ".czi")|| endsWith(path, ".lif")) run("Bio-Formats", "open=["+path+"] color_mode=Composite rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
else if (endsWith(path, ".tif")|| endsWith(path, ".tiff")) open(path);
else exit("File type not recognised. Tif, Lif and CZI files supported.");
dir=File.directory;
file_name=File.nameWithoutExtension; //get file name without extension (.lif)
}

file_name_length=lengthOf(file_name);
if(file_name_length>50) file_name=substring(file_name, 0, 39); //Restricting file name length as in Windows long path names can cause errors
else if (endsWith(path, ".lif"))
{
run("Bio-Formats Macro Extensions");
Ext.setId(path);
Ext.getSeriesCount(seriesCount);
print("Opening lif file, detected series count of "+seriesCount+". Leave options in bioformats importer unticked");
open(path);

}
else if (endsWith(path, ".tif")|| endsWith(path, ".tiff")) open(path);
else exit("File type not recognised. Tif, Lif and Czi files supported.");
dir=File.directory;
file_name_full=File.nameWithoutExtension; //get file name without extension (.lif)
}

//file_name=File.nameWithoutExtension;
file_name_length=lengthOf(file_name_full);
if(file_name_length>50)
{
file_name=substring(file_name_full, 0, 20); //Restricting file name length as in Windows long path names can cause errors
suffix = getString("File name is too long, so it will be truncated. Enter custom name to be be added to end of filename", "_1");
file_name = file_name+suffix;
}
else file_name=file_name_full;
//if delimiters such as , ; or _ are there in file name, split string and join with underscore
file_name_split = split(file_name,",;_-");
file_name =String.join(file_name_split,"_");


img_name=getTitle();
Stack.getDimensions(width, height, sizeC, sizeZ, frames);
max_save_name="MAX_"+file_name;
Expand Down Expand Up @@ -202,12 +220,11 @@ if(scale_factor<1.001 && scale_factor>1) scale_factor=1;
print("Analysing: "+file_name);
analysis_dir= dir+"Analysis"+fs;
if (!File.exists(analysis_dir)) File.makeDirectory(analysis_dir);
print("Files will be saved at: "+analysis_dir);

//Create results directory with file name in "analysis"
results_dir=analysis_dir+file_name+fs; //directory to save images
if (!File.exists(results_dir)) File.makeDirectory(results_dir); //create directory to save results file

print("Files will be saved at: "+results_dir);

//do not include cells greater than 1000 micron in area
//neuron_area_limit=1500; //microns
neuron_max_pixels=neuron_area_limit/pixelWidth; //convert micron to pixels
Expand Down Expand Up @@ -264,7 +281,12 @@ else
print(img_name+" has only one slice, using as max projection");
max_projection=getTitle();
}


max_save_name="MAX_"+file_name;
selectWindow(max_projection);
rename(max_save_name);

max_projection = max_save_name;



Expand Down
97 changes: 70 additions & 27 deletions _Analyse Neuron (Multi-channel).ijm
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Original file line number Diff line number Diff line change
Expand Up @@ -166,27 +166,44 @@ if(marker_subtype==1 && Enter_channel_details_now==1)




if(image_already_open==true)
{
waitForUser("Select Image. and choose output folder in next prompt");
file_name=getTitle(); //get file name without extension (.lif)
dir=getDirectory("Choose Output Folder");

}
else
{
if(endsWith(path, ".czi")|| endsWith(path, ".lif")) run("Bio-Formats", "open=["+path+"] color_mode=Composite rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
else if (endsWith(path, ".tif")|| endsWith(path, ".tiff")) open(path);
else exit("File type not recognised. Tif, Lif and CZI files supported.");
dir=File.directory;
file_name=File.nameWithoutExtension; //get file name without extension (.lif)
}

file_name_length=lengthOf(file_name);
if(file_name_length>50) file_name=substring(file_name, 0, 39); //Restricting file name length as in Windows long path names can cause errors
if(image_already_open==true)
{
waitForUser("Select Image and choose output folder in next prompt");
file_name_full=getTitle(); //get file name without extension (.lif)
dir=getDirectory("Choose Output Folder");
}
else
{
if(endsWith(path, ".czi")) run("Bio-Formats", "open=["+path+"] color_mode=Composite rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
else if (endsWith(path, ".lif"))
{
run("Bio-Formats Macro Extensions");
Ext.setId(path);
Ext.getSeriesCount(seriesCount);
print("Opening lif file, detected series count of "+seriesCount+". Leave options in bioformats importer unticked");
open(path);

}
else if (endsWith(path, ".tif")|| endsWith(path, ".tiff")) open(path);
else exit("File type not recognised. Tif, Lif and Czi files supported.");
dir=File.directory;
file_name_full=File.nameWithoutExtension; //get file name without extension (.lif)
}

//file_name=File.nameWithoutExtension;
file_name_length=lengthOf(file_name_full);
if(file_name_length>50)
{
file_name=substring(file_name_full, 0, 20); //Restricting file name length as in Windows long path names can cause errors
suffix = getString("File name is too long, so it will be truncated. Enter custom name to be be added to end of filename", "_1");
file_name = file_name+suffix;
}
else file_name=file_name_full;
//if delimiters such as , ; or _ are there in file name, split string and join with underscore
file_name_split = split(file_name,",;_-");
file_name =String.join(file_name_split,"_");



img_name=getTitle();
Stack.getDimensions(width, height, sizeC, sizeZ, frames);

Expand Down Expand Up @@ -233,12 +250,11 @@ if(scale_factor<1.001 && scale_factor>1) scale_factor=1;
print("Analysing: "+file_name);
analysis_dir= dir+"Analysis"+fs;
if (!File.exists(analysis_dir)) File.makeDirectory(analysis_dir);
print("Files will be saved at: "+analysis_dir);

//Create results directory with file name in "analysis"
results_dir=analysis_dir+file_name+fs; //directory to save images
if (!File.exists(results_dir)) File.makeDirectory(results_dir); //create directory to save results file

print("Files will be saved at: "+results_dir);

//do not include cells greater than 1000 micron in area
//neuron_area_limit=1500; //microns
neuron_max_pixels=neuron_area_limit/pixelWidth; //convert micron to pixels
Expand Down Expand Up @@ -376,7 +392,11 @@ else
print(img_name+" has only one slice, using as max projection");
max_projection=getTitle();
}

max_save_name="MAX_"+file_name;
selectWindow(max_projection);
rename(max_save_name);

max_projection = max_save_name;



Expand Down Expand Up @@ -461,10 +481,16 @@ selectWindow(neuron_label_image);
run("Select None");

print("No of "+cell_type+" in "+max_projection+" : "+cell_count);

//select all rois in roi manager
selection_indexes = Array.getSequence(roiManager("count"));
roiManager("select", selection_indexes);
group_id = 1;
set_all_rois_group_id(group_id);
roiManager("deselect");
roi_location=results_dir+cell_type+"_ROIs_"+file_name+".zip";
roiManager("save",roi_location );

selectWindow(table_name);
Table.set("File name",row,file_name);
Table.set("Total "+cell_type, row, cell_count); //set total count of neurons after nos analysis if nos selected
Expand Down Expand Up @@ -674,7 +700,7 @@ if(marker_subtype==1)
//keep objects within size range 400 to 3000; may need to alter this later depending on cell size
//Manual step to verify
temp_label=multiply_markers(neuron_label_image,"label_img_temp",neuron_min_pixels,neuron_max_pixels);//getting smaller objects, so inc min size to 400
//decide on how to work with multiplication, neuron multiply labl or other way around?

//selectWindow(temp_label);
selectWindow(temp_label);
run("Select None");
Expand All @@ -686,7 +712,13 @@ if(marker_subtype==1)
//roiManager("deselect");
roiManager("show all");
//selectWindow(max_projection);
//add option to draw ROI on channel name OR
//display Hu and other channel as overlay; assign groups with different colours;
//get user to click
waitForUser("Verify ROIs for "+channel_name+". Delete or add ROIs as needed. Press OK when done.");

group_id+=1;
set_all_rois_group_id(group_id);
roiManager("deselect");
//convert roi manager to label image
runMacro(roi_to_label);
Expand Down Expand Up @@ -1354,4 +1386,15 @@ function create_ganglia_img(max_projection,ganglia_channel,cell_channel)
return ganglia_rgb;


}
}

//set group id for rois
function set_all_rois_group_id(group_id)
{

//select all rois in roi manager
selection_indexes = Array.getSequence(roiManager("count"));
roiManager("select", selection_indexes);
RoiManager.setGroup(0);
}

Expand Down
44 changes: 33 additions & 11 deletions _Analyse Neurons.ijm
View file
Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,16 @@ if(image_already_open==true)
}
else
{
if(endsWith(path, ".czi")|| endsWith(path, ".lif")) run("Bio-Formats", "open=["+path+"] color_mode=Composite rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
if(endsWith(path, ".czi")) run("Bio-Formats", "open=["+path+"] color_mode=Composite rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT");
else if (endsWith(path, ".lif"))
{
run("Bio-Formats Macro Extensions");
Ext.setId(path);
Ext.getSeriesCount(seriesCount);
print("Opening lif file, detected series count of "+seriesCount+". Leave options in bioformats importer unticked");
open(path);

}
else if (endsWith(path, ".tif")|| endsWith(path, ".tiff")) open(path);
else exit("File type not recognised. Tif, Lif and Czi files supported.");
dir=File.directory;
Expand All @@ -130,9 +139,18 @@ else

//file_name=File.nameWithoutExtension;
file_name_length=lengthOf(file_name_full);
if(file_name_length>50) file_name=substring(file_name_full, 0, 39); //Restricting file name length as in Windows long path names can cause errors
if(file_name_length>50)
{
file_name=substring(file_name_full, 0, 20); //Restricting file name length as in Windows long path names can cause errors
suffix = getString("File name is too long, so it will be truncated. Enter custom name to be be added to end of filename", "_1");
file_name = file_name+suffix;
}
else file_name=file_name_full;
//print(file_name);
//if delimiters such as , ; or _ are there in file name, split string and join with underscore
file_name_split = split(file_name,",;_-");
file_name =String.join(file_name_split,"_");

print(file_name);

img_name=getTitle();
Stack.getDimensions(width, height, sizeC, sizeZ, frames);
Expand Down Expand Up @@ -178,12 +196,11 @@ if(scale_factor<1.001 && scale_factor>1) scale_factor=1;
print("Analysing: "+file_name);
analysis_dir= dir+"Analysis"+fs;
if (!File.exists(analysis_dir)) File.makeDirectory(analysis_dir);
print("Files will be saved at: "+analysis_dir);
print("Analysing: "+file_name);
//Create results directory with file name in "analysis"
results_dir=analysis_dir+file_name+fs; //directory to save images
if (!File.exists(results_dir)) File.makeDirectory(results_dir); //create directory to save results file

print("Files will be saved at: "+results_dir);

//do not include cells greater than 1000 micron in area
//neuron_area_limit=1500; //microns
Expand Down Expand Up @@ -308,7 +325,9 @@ else
}

max_save_name="MAX_"+file_name;

selectWindow(max_projection);
rename(max_save_name);
max_projection = max_save_name;

//Segment Neurons
selectWindow(max_projection);
Expand Down Expand Up @@ -384,12 +403,9 @@ roiManager("deselect");
print("No of "+cell_type+" in "+max_projection+" : "+cell_count);
roiManager("deselect");
roi_location=results_dir+cell_type+"_ROIs_"+file_name+".zip";
roiManager("save",roi_location );


roiManager("save",roi_location);


selectWindow(max_projection);
selectWindow(max_projection);

//uses roi to label macro code; clij is a dependency
runMacro(roi_to_label);
Expand Down Expand Up @@ -532,6 +548,12 @@ if(Save_Image_Masks == true)
}
}

//save max projection if its scaled image, can use this for further processing later
selectWindow(max_projection);
run("Remove Overlay");
run("Select None");
saveAs("Tiff", results_dir+max_save_name);


close("*");
exit("Neuron analysis complete");
Expand Down

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