Fiji>Image>Overlay>List elements returns only the first 63 independent points of many more

[lollopus]

The issue came up with an output file of Alex Herbert's FindFoci plugin, when using the option to label maxima as overlay points. In particular I have an image with 300 points, but the List elements command in Fiji returns only the first 63!

0	null	Point	126	4851	1	1	cyan	yellow	1	14	0	14	0
1	null	Point	123	5721	1	1	cyan	yellow	1	18	0	18	0
2	null	Point	1409	1256	1	46	cyan	yellow	1	21	0	21	0
3	null	Point	1409	1212	1	1	cyan	yellow	1	22	0	22	0
4	null	Point	18	3805	1	1	cyan	yellow	1	24	0	24	0
5	null	Point	117	5728	1	1	cyan	yellow	1	27	0	27	0
6	null	Point	539	5791	1	1	cyan	yellow	1	40	0	40	0
7	null	Point	20	1940	1	1	cyan	yellow	1	43	0	43	0
8	null	Point	108	4858	1	1	cyan	yellow	1	44	0	44	0
9	null	Point	257	4857	622	146	cyan	yellow	1	47	0	47	0
10	null	Point	606	1135	804	3826	cyan	yellow	1	48	0	48	0
11	null	Point	621	5029	1	1	cyan	yellow	1	49	0	49	0
12	null	Point	485	5039	264	21	cyan	yellow	1	50	0	50	0
13	null	Point	637	4914	216	878	cyan	yellow	1	51	0	51	0
14	null	Point	508	5146	1	1	cyan	yellow	1	53	0	53	0
15	null	Point	1401	3387	3	44	cyan	yellow	1	54	0	54	0
16	null	Point	496	5389	1	1	cyan	yellow	1	55	0	55	0
17	null	Point	17	3387	21	456	cyan	yellow	1	56	0	56	0
18	null	Point	19	209	308	2533	cyan	yellow	1	57	0	57	0
19	null	Point	17	2702	613	2692	cyan	yellow	1	58	0	58	0
20	null	Point	155	4531	1	1	cyan	yellow	1	59	0	59	0
21	null	Point	18	1847	624	3524	cyan	yellow	1	61	0	61	0
22	null	Point	158	3965	1188	1632	cyan	yellow	1	62	0	62	0
23	null	Point	81	4255	99	307	cyan	yellow	1	63	0	63	0
24	null	Point	147	3921	1257	562	cyan	yellow	1	64	0	64	0
25	null	Point	143	3898	1214	683	cyan	yellow	1	65	0	65	0
26	null	Point	55	3878	1307	658	cyan	yellow	1	66	0	66	0
27	null	Point	21	1548	1390	2697	cyan	yellow	1	67	0	67	0
28	null	Point	68	924	1341	3676	cyan	yellow	1	68	0	68	0
29	null	Point	105	4387	143	606	cyan	yellow	1	69	0	69	0
30	null	Point	70	4279	76	241	cyan	yellow	1	70	0	70	0
31	null	Point	21	1752	230	4005	cyan	yellow	1	71	0	71	0
32	null	Point	35	4179	235	879	cyan	yellow	1	72	0	72	0
33	null	Point	18	1515	1393	4187	cyan	yellow	1	73	0	73	0
34	null	Point	19	1867	108	2508	cyan	yellow	1	74	0	74	0
35	null	Point	150	4825	1004	218	cyan	yellow	1	75	0	75	0
36	null	Point	89	4411	134	1382	cyan	yellow	1	76	0	76	0
37	null	Point	14	3757	1108	1624	cyan	yellow	1	77	0	77	0
38	null	Point	15	4249	226	1544	cyan	yellow	1	78	0	78	0
39	null	Point	30	4243	192	1550	cyan	yellow	1	79	0	79	0
40	null	Point	84	4737	1049	1056	cyan	yellow	1	80	0	80	0
41	null	Point	29	4019	184	1625	cyan	yellow	1	81	0	81	0
42	null	Point	12	1338	1399	4040	cyan	yellow	1	82	0	82	0
43	null	Point	20	4336	181	1425	cyan	yellow	1	83	0	83	0
44	null	Point	17	3866	1129	1916	cyan	yellow	1	84	0	84	0
45	null	Point	13	4253	215	1459	cyan	yellow	1	85	0	85	0
46	null	Point	75	4346	1098	1416	cyan	yellow	1	86	0	86	0
47	null	Point	18	3705	186	2073	cyan	yellow	1	87	0	87	0
48	null	Point	18	3823	156	1868	cyan	yellow	1	88	0	88	0
49	null	Point	18	3739	219	2040	cyan	yellow	1	89	0	89	0
50	null	Point	64	4854	173	905	cyan	yellow	1	90	0	90	0
51	null	Point	18	3837	211	1941	cyan	yellow	1	91	0	91	0
52	null	Point	18	3848	168	1944	cyan	yellow	1	92	0	92	0
53	null	Point	43	4841	198	906	cyan	yellow	1	93	0	93	0
54	null	Point	98	4918	566	703	cyan	yellow	1	94	0	94	0
55	null	Point	17	3882	113	1803	cyan	yellow	1	95	0	95	0
56	null	Point	132	5382	46	313	cyan	yellow	1	96	0	96	0
57	null	Point	145	4990	514	733	cyan	yellow	1	97	0	97	0
58	null	Point	10	5617	145	80	cyan	yellow	1	98	0	98	0
59	null	Point	170	4848	92	881	cyan	yellow	1	99	0	99	0
60	null	Point	21	5301	145	455	cyan	yellow	1	100	0	100	0
61	null	Point	153	5358	67	402	cyan	yellow	1	101	0	101	0
62	null	Point	724	5334	1	1	cyan	yellow	1	105	0	105	0

[rasband]

Please provide a minimal and complete example that reproduces this problem. Something like the following JavaScript that lists 5000 points.

  n = 5000;
  w = 1000, h = 700;
  img = IJ.createImage("Demo","8-bit black",w,h,1);
  ran = new Random();
  overlay = new Overlay();
  for (i=0; i<n; i++) {
      x = ran.nextFloat()*w;
      y = ran.nextFloat()*h;
      overlay.add(new PointRoi(x,y));
  }
  img.setOverlay(overlay);
  img.show();
  IJ.run("List Elements", "");

[lollopus]

I cannot reproduce this programmatically so I'll repost this issue in Alex's GSDC repository instead.

Sorry @rasband

[imagejan]

For the record, the new issue is now here: aherbert/gdsc#5

[lollopus]

I'm reporting here the results of my interaction with Alex Herbert on this issue.

There is no bug either in ImageJ or FindFoci: FindFoci labels maxima by adding a PointRoi as an overlay for each slice of the image stack. Each of these PointRois may, in turn, contain one or more point maxima.

I did not realize this when I examined the output table of the ListElements command, wrongly assuming that each line of the table consisted of just 1 point.

This brings me to a feature enhancement suggestion: to add in the results table a column for the .npoints field of any PolygonRois present in the overlay. This would avoid any confusion such as the one in which I incurred.

[rasband]

The latest ImageJ daily build (1.52h31) adds a "Points" column to the Image>Overlay>List Elements table. View the code changes at d320de6.