I am still doing it very crudely and am myself trying to find a way to connect the two together. I will let you know if I get any success !

I'm veering off-topic though.

I would, of course, like to see the image processing functionality improve too. I would like to see common tools be included as built-in functions.

My point was simply that there will always be many more tools that Wolfram won't have resources to include. Like you, I love to work in Mathematica, so I hope they'll make it as easy as possible to use Mathematica as a glue language and call other systems directly from Mathematica as needed. E.g. J/Link is already very good, but alone it's not enough.

Btw this version of the function written by someone (forgot the name) is slow but sometimes I find it useful:

HistogramTransformationWeightedLocalAdaptive[img_, radius_] := 
  Module[{funs, nodes, w, h, f, fun, fi},
   funs = Map[HistogramTransformInterpolation, ImagePartition[img, {2*radius + 1}], {2}];
   {w, h} = ImageDimensions@img;
   nodes = Map[Mean@Flatten[N@ImageData[#, Automatic], 1] &, 
     ImagePartition[Image[Array[{#1, #2} &, {h, w}], "Bit16"], {2*radius + 1}], {2}];
   nodes = ArrayPad[nodes, {{1, 1}, {1, 1}}, "Fixed"];
   nodes[[All, {1, -1}, 2]] = {1, w};
   nodes[[{1, -1}, All, 1]] = {1, h};
   funs = ArrayPad[funs, 1, "Fixed"];
   fi = Interpolation[Thread[{Round@Flatten[nodes, 1], 
       Table[f[#], {f, Flatten@funs}]}], InterpolationOrder -> 1];
   fun[v_, {r_, c_}] := Evaluate[fi[r, c]] &[v];
   Quiet@ImageApplyIndexed[fun, img]
   ];

Can you clarify what you mean by 16-bit image display?

As for Fiji, I asked a question about interoperability here:

• https://mathematica.stackexchange.com/questions/180513/using-imagej-filters-directly-from-mathematica-through-j-link

Mathematica can't be expected to have everything Fiji has (especially special plugins!) but it would be great if I could use Mathematica as the centre of my workflow and still employ ImageJ for certain specific tasks. It seems that J/Link currently has some limitations that make it difficult to use ImageJ (and I now knowing much Java didn't help ...) I wrote to Wolfram Support about this and the feedback I got so far sounded encouraging (i.e. that they'd look into making things work). Let's see how that works out!

I also have a small LTemplate-based framework to make it easier to call SimpleITK functions directly from Mathematica. Sometimes SimpleITK has useful stuff that Mathematica doesn't (e.g. local histogram equalization, which I hope Mathematica will get in the future).

Occasionally I use MATLAB stuff too through MATLink.

Overall, what I am wishing for the most is better interoperability with other systems.

If some operation is built-in, that's obviously the best. But Wolfram only has limited resources. A high-quality interface to other systems, or toolkits that make it easier to build such interfaces (like LTemplate), can often give the highest benefit for the least amount of work.

Thanks Sander ! was really hidden :)

i know that the first one is already there, albeit a bit hidden:

ClearAll[oFindImageCircles]
oFindImageCircles[img_/;ImageQ@img&&ImageChannels@img==1,
{sizemin_Integer,sizemax_Integer},(*range of radii for circles*)
mindist_Real,(*minimum distance in between circle centers*)
thrCanny_Real,(*minimum canny edge strength---the function computes edge detection on the input*)
thrStrength_Real,(*minimum strength of circle (aka votes)*)
resolutionfactor_,(*between 0 and 1,how big is the hough array compared to the image*)
nmax_  (*max number of circles*)
]:=Module[{res},Needs["OpenCVLink`"];
    res=OpenCVLink`Private`$HoughCircles[img,1/resolutionfactor,mindist,(255*thrCanny),thrStrength,sizemin,sizemax];(*sorted by strength already*)
    If[Head@res=!=List,Throw@$Failed];
        res={{#1,#2},#3}&@@@Partition[res,3];
        If[nmax===All,
            res,
            Take[res,UpTo[nmax]]
        ]
];