How to convert Imaris mask .tif for HistoCAT

Dear forum participant,

I would like to use an Imaris generated mask in HistoCAT. The Imaris export of the segmented cells generates a .tif with rainbow colored objects. However HistoCAT prefers a unit 16 mask that is more similiar to the CellProfiler mask file format, basicly just the outlines of the objects.

Does anyone know how to convert a .tif of dense rainbow objects to instead object outlines?

Thanks in advance for any advice,
Ann

Hi @ANNHABERMAN,

welcome on the forum!
In ImageJ/FIJI, you could try to Threshold your image and use the Analyse Particles with the option Bare Outlines in the show dropdown menu.

Please, find below a small imagej macro that will generate a rainbow-like image from blobs and create the outline image.

// open the blobs image and threshold it
run("Blobs (25K)");
run("Invert LUT");
setAutoThreshold("Default dark");
setOption("BlackBackground", true);
run("Convert to Mask");

// use analyse particles with the output "Count Masks"
run("Analyze Particles...", "  show=[Count Masks] exclude");
selectImage(nImages);
run("glasbey_inverted");
// So you get a rainbow-like series of objects

// threshold and use the Bare Outlines output
setThreshold(1, 65535);
run("Analyze Particles...", "  show=[Bare Outlines]");
run("Invert");

// to convert the image to 16-bit
make16bit = true ;
if (make16bit) run("16-bit");

image

If you are looking for something different, could you provide a link to dowload one of your image ?

Cheers,

Romain