gin commit from ma-macpro-server.local

New files: 93
Modified files: 11

ARA/acronyms_parent.txt

@@ -0,0 +1,49 @@
+22	PTLp
+31	ACA
+44	ILA
+95	AI
+184	FRP
+247	AUD
+254	RSP
+275	LSX
+278	sAMY
+313	MB
+329	SSp-bfd
+337	SSp-ll
+345	SSp-m
+353	SSp-n
+354	MY
+361	SSp-tr
+369	SSp-ul
+378	SSs
+485	STRd
+493	STRv
+519	CBN
+528	CBX
+541	TEa
+583	CLA
+669	VIS
+677	VISC
+698	OLF
+703	CTXsp
+714	ORB
+771	P
+776	cc
+784	cst
+803	PAL
+822	RHP
+856	DORpm
+864	DORsm
+895	ECT
+896	lfbst
+922	PERI
+967	cm
+972	PL
+985	MOp
+991	mfbs
+993	MOs
+1000	eps
+1057	GU
+1080	HIP
+1097	HY
+1098	SSp-un

ARA/acronyms_parent_splitted.txt

@@ -0,0 +1,98 @@
+22	L_PTLp
+31	L_ACA
+44	L_ILA
+95	L_AI
+184	L_FRP
+247	L_AUD
+254	L_RSP
+275	L_LSX
+278	L_sAMY
+313	L_MB
+329	L_SSp-bfd
+337	L_SSp-ll
+345	L_SSp-m
+353	L_SSp-n
+354	L_MY
+361	L_SSp-tr
+369	L_SSp-ul
+378	L_SSs
+485	L_STRd
+493	L_STRv
+519	L_CBN
+528	L_CBX
+541	L_TEa
+583	L_CLA
+669	L_VIS
+677	L_VISC
+698	L_OLF
+703	L_CTXsp
+714	L_ORB
+771	L_P
+776	L_cc
+784	L_cst
+803	L_PAL
+822	L_RHP
+856	L_DORpm
+864	L_DORsm
+895	L_ECT
+896	L_lfbst
+922	L_PERI
+967	L_cm
+972	L_PL
+985	L_MOp
+991	L_mfbs
+993	L_MOs
+1000	L_eps
+1057	L_GU
+1080	L_HIP
+1097	L_HY
+1098	L_SSp-un
+2022	R_PTLp
+2031	R_ACA
+2044	R_ILA
+2095	R_AI
+2184	R_FRP
+2247	R_AUD
+2254	R_RSP
+2275	R_LSX
+2278	R_sAMY
+2313	R_MB
+2329	R_SSp-bfd
+2337	R_SSp-ll
+2345	R_SSp-m
+2353	R_SSp-n
+2354	R_MY
+2361	R_SSp-tr
+2369	R_SSp-ul
+2378	R_SSs
+2485	R_STRd
+2493	R_STRv
+2519	R_CBN
+2528	R_CBX
+2541	R_TEa
+2583	R_CLA
+2669	R_VIS
+2677	R_VISC
+2698	R_OLF
+2703	R_CTXsp
+2714	R_ORB
+2771	R_P
+2776	R_cc
+2784	R_cst
+2803	R_PAL
+2822	R_RHP
+2856	R_DORpm
+2864	R_DORsm
+2895	R_ECT
+2896	R_lfbst
+2922	R_PERI
+2967	R_cm
+2972	R_PL
+2985	R_MOp
+2991	R_mfbs
+2993	R_MOs
+3000	R_eps
+3057	R_GU
+3080	R_HIP
+3097	R_HY
+3098	R_SSp-un

ARA/annotation_10.nii.gz

@@ -0,0 +1 @@
+/annex/objects/MD5-s35125022--2b8ba38fc3fa5d7f63679357cc9e450a

ARA/annotation_10_parent.nii.gz

@@ -0,0 +1 @@
+/annex/objects/MD5-s24824984--23adab85404680509a91e3bed9d81c6b

ARA/annotation_10_parent_splitted.nii.gz

@@ -0,0 +1 @@
+/annex/objects/MD5-s25279898--0e8c51e926a8f16ecfb32851bfdc7b1c

ARA/annotation_10_splitted.nii.gz

@@ -0,0 +1 @@
+/annex/objects/MD5-s33719985--3c0cb1912435f0121979ae28dd8d9b48

ARA/template_10.nii.gz

@@ -0,0 +1 @@
+/annex/objects/MD5-s435607530--bf4266ccbe79128d9184fc45fd89c556

Test_Images/GFAP_highResolutionCH_2.txt

@@ -0,0 +1,236 @@
+AIDAhisto - Number of detected cells: 233
+cell postions (xy):
+
+4 279
+5 709
+6 634
+7 609
+20 642
+24 112
+25 729
+29 157
+33 620
+33 691
+35 671
+37 527
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+553 138
+553 447
+553 695
+554 88
+554 227
+555 24
+555 162

Test_Images/GFAP_highResolutionCH_2_v.txt

@@ -0,0 +1,131 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells 128 
+x-y Cell Postitions 
+4 279
+5 709
+24 112
+25 729
+29 157
+33 691
+35 671
+43 650
+49 682
+68 587
+75 510
+78 214
+98 65
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+135 423
+153 75
+162 410
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+171 685
+173 384
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+536 715
+551 498
+552 581
+552 630
+553 138
+553 447
+553 695

Test_Images/GFAP_highResolutionCH_3.txt

@@ -0,0 +1,277 @@
+AIDAhisto - Number of detected cells: 274
+cell postions (xy):
+
+3 274
+4 130
+4 182
+4 215
+4 253
+4 389
+7 450
+7 671
+10 88
+10 304
+18 707
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Test_Images/GFAP_lowResolution.tif_process.log

@@ -0,0 +1 @@
+['-f', '/Volumes/AG_Aswendt_Share/Scratch/Shared_Software/Github/AIDAhisto_v1.1/testImages/GFAP_lowResolution.tif', '-o', '/Volumes/AG_Aswendt_Projects/TVA_Thrombin/Histology/Z_E2_4/Z_E2_4_3/Z_E_2_4_3_Slide_17_Cy3/testoutput/t']

Test_Images/GFAP_lowResolutionCH_1.txt

@@ -0,0 +1,73 @@
+AIDAhisto - Number of detected cells: 70
+cell postions (xy):
+
+4 29
+6 71
+11 44
+11 92
+13 21
+13 98
+13 118
+19 32
+23 73
+25 80
+26 106
+30 45
+30 86
+31 98
+33 14
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+44 8
+44 25
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+79 25
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+84 100
+91 110
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+96 105
+99 93
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+119 85
+119 102
+121 58
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+124 68
+126 46
+126 86
+126 114
+127 19
+129 73
+133 24
+133 37
+133 66

Test_Images/GFAP_lowResolutionCH_1_v.txt

@@ -0,0 +1,64 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells 61 
+x-y Cell Postitions 
+4 29
+6 71
+11 44
+11 92
+13 21
+13 98
+13 118
+19 32
+23 73
+25 80
+30 45
+30 86
+31 98
+33 14
+36 24
+36 118
+44 8
+44 25
+50 5
+58 51
+59 119
+61 24
+61 98
+62 79
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+64 60
+66 46
+66 66
+67 110
+68 16
+72 23
+75 108
+82 7
+83 43
+84 28
+84 100
+91 110
+93 31
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+109 61
+110 26
+111 48
+111 112
+114 94
+119 85
+119 102
+121 58
+122 119
+126 46
+126 86
+127 19
+129 73
+133 24
+133 37
+133 66

Test_Images/GFAP_lowResolutionCH_3.txt

@@ -0,0 +1,210 @@
+AIDAhisto - Number of detected cells: 207
+cell postions (xy):
+
+1 29
+3 37
+3 54
+4 13
+4 23
+6 121
+8 50
+8 63
+8 70
+8 80
+9 4
+9 104
+11 56
+11 88
+12 18
+13 116
+15 48
+15 84
+16 62
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+17 17
+17 121
+18 22
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+18 109
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+19 72
+22 79
+23 7
+25 19
+25 119
+26 31
+26 98
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+30 45
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+31 81
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+34 7
+34 56
+34 75
+35 63
+35 95
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+36 115
+38 68
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+41 4
+41 28
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+44 43
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+45 26
+45 67
+45 105
+48 122
+49 5
+49 50
+50 26
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+51 41
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+59 73
+60 123
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+62 65
+62 98
+62 103
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+64 72
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+66 52
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+80 17
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+83 46
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+91 72
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+92 7
+92 25
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+95 2
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+128 25
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+131 123
+133 24
+133 34
+133 110
+134 69
+134 86
+135 120
+138 31
+138 91

Test_Images/GFAP_lowResolution_ch1_cC.txt

@@ -0,0 +1,157 @@
+Number of detected cells: 154
+cell postions (xy):
+
+2	10
+2	33
+2	90
+2	106
+2	133
+3	81
+3	117
+4	65
+5	105
+6	16
+6	51
+7	28
+9	45
+12	93
+13	103
+13	117
+13	138
+15	2
+15	15
+15	34
+16	115
+17	49
+17	69
+18	116
+20	128
+21	94
+22	14
+22	87
+22	122
+24	73
+25	37
+25	62
+25	134
+26	45
+26	80
+27	111
+30	5
+32	94
+33	20
+33	53
+34	93
+35	31
+35	44
+36	120
+40	47
+40	62
+40	76
+40	103
+42	137
+44	84
+44	120
+45	12
+46	2
+46	31
+46	53
+47	67
+47	127
+49	112
+50	51
+50	94
+52	14
+52	59
+52	104
+55	24
+56	80
+57	138
+58	40
+59	3
+59	122
+61	65
+61	100
+62	72
+62	110
+64	50
+65	34
+66	3
+67	134
+68	92
+69	65
+69	101
+72	7
+73	47
+73	130
+74	24
+75	34
+76	102
+76	121
+77	16
+78	94
+78	138
+79	75
+80	63
+81	26
+81	43
+83	110
+85	2
+86	10
+86	51
+86	120
+87	31
+87	44
+87	127
+89	63
+90	137
+91	82
+93	51
+93	77
+94	100
+95	20
+95	115
+97	2
+99	14
+99	32
+99	77
+99	130
+101	85
+103	2
+103	120
+104	60
+104	138
+105	124
+106	97
+107	11
+107	49
+107	105
+108	61
+109	76
+111	68
+111	92
+112	9
+113	112
+114	33
+114	55
+115	138
+116	24
+116	98
+117	44
+119	14
+119	37
+119	137
+120	3
+120	60
+120	123
+124	129
+125	16
+125	45
+125	84
+126	13
+126	29
+126	55
+126	77
+126	95
+126	111
+126	120

Test_Images/GFAP_lowResolution_ch3_cC.txt

@@ -0,0 +1,289 @@
+Number of detected cells: 286
+cell postions (xy):
+
+2	16
+2	31
+2	53
+2	61
+2	69
+2	89
+2	96
+2	102
+2	127
+2	138
+3	109
+3	116
+4	2
+4	10
+4	42
+5	132
+6	50
+7	72
+7	102
+8	24
+8	35
+8	79
+8	93
+9	38
+9	111
+10	105
+11	138
+12	70
+12	121
+13	33
+13	66
+13	79
+13	83
+13	100
+14	4
+14	38
+14	87
+16	106
+16	132
+17	46
+17	112
+17	127
+18	18
+18	81
+18	117
+19	13
+19	37
+19	75
+19	96
+20	26
+21	1
+21	108
+22	41
+22	53
+22	86
+22	122
+23	19
+23	31
+23	68
+24	5
+24	115
+25	134
+26	62
+26	93
+26	129
+27	46
+27	51
+27	101
+27	111
+28	57
+29	42
+29	108
+30	2
+30	20
+30	122
+31	15
+31	76
+31	131
+32	27
+32	138
+33	48
+34	83
+34	97
+35	41
+35	53
+35	134
+36	88
+38	4
+38	15
+38	45
+39	111
+39	128
+40	79
+40	116
+41	93
+41	98
+42	13
+42	33
+42	52
+42	63
+42	123
+43	105
+44	2
+44	45
+44	128
+45	137
+46	31
+47	49
+47	84
+47	132
+48	96
+49	16
+50	2
+50	57
+50	111
+51	9
+51	50
+53	62
+53	67
+53	131
+54	77
+55	4
+56	71
+56	106
+57	12
+57	19
+57	35
+57	85
+58	132
+59	43
+59	138
+60	55
+60	81
+61	65
+61	100
+61	133
+62	108
+63	17
+63	90
+64	9
+64	36
+64	51
+64	122
+65	2
+66	63
+66	83
+67	74
+68	46
+68	68
+68	94
+69	31
+69	39
+70	102
+70	129
+70	136
+71	5
+71	9
+72	52
+73	20
+73	65
+73	76
+73	92
+73	118
+74	60
+74	130
+75	101
+76	3
+76	35
+79	17
+79	40
+79	67
+79	105
+80	23
+80	130
+81	9
+81	46
+81	56
+81	62
+81	93
+81	113
+82	32
+82	51
+83	2
+83	136
+84	119
+85	16
+85	37
+85	69
+85	106
+86	73
+86	78
+86	83
+86	125
+87	28
+87	54
+87	135
+88	2
+89	12
+89	19
+89	42
+90	86
+91	79
+92	127
+92	138
+94	2
+94	99
+94	131
+95	21
+95	67
+96	36
+96	52
+96	76
+96	89
+96	124
+97	16
+97	85
+97	132
+98	101
+99	2
+99	27
+99	63
+99	70
+100	115
+101	56
+101	127
+102	81
+103	138
+104	63
+104	91
+105	3
+105	10
+105	34
+105	97
+105	117
+105	132
+106	46
+106	86
+106	128
+108	55
+108	122
+109	71
+109	108
+110	19
+110	83
+111	75
+111	100
+112	2
+112	10
+112	92
+114	67
+114	108
+114	136
+115	31
+115	113
+116	37
+117	14
+117	44
+118	52
+119	2
+119	59
+119	81
+119	123
+120	26
+120	39
+120	128
+121	67
+121	104
+121	113
+121	137
+122	7
+122	18
+124	49
+124	86
+124	94
+124	132
+125	3
+125	27
+125	40
+125	61
+126	13
+126	34
+126	52
+126	79
+126	106
+126	118
+126	124

Test_Images/IBA1_highResolutionCH_1.txt

@@ -0,0 +1,32 @@
+AIDAhisto - Number of detected cells: 29
+cell postions (xy):
+
+7 572
+9 699
+10 202
+32 686
+57 546
+62 230
+82 436
+87 8
+132 570
+153 560
+183 393
+226 165
+227 504
+288 606
+316 122
+338 509
+346 375
+351 697
+377 525
+378 341
+426 251
+455 32
+488 70
+493 549
+503 240
+538 153
+541 79
+541 388
+541 423

Test_Images/IBA1_highResolutionCH_1_v.txt

@@ -0,0 +1,23 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells 20 
+x-y Cell Postitions 
+10 202
+57 546
+62 230
+82 436
+87 8
+132 570
+183 393
+226 165
+227 504
+288 606
+338 509
+346 375
+351 697
+377 525
+378 341
+426 251
+455 32
+493 549
+503 240
+538 153

Test_Images/IBA1_highResolutionCH_3.txt

@@ -0,0 +1,257 @@
+AIDAhisto - Number of detected cells: 254
+cell postions (xy):
+
+4 203
+4 281
+6 437
+7 239
+7 489
+11 411
+17 34
+19 368
+20 7
+20 327
+21 641
+28 620
+30 124
+31 222
+32 395
+35 191
+38 165
+41 585
+42 247
+42 343
+44 51
+44 285
+46 537
+54 453
+54 511
+59 347
+60 651
+62 37
+67 216
+70 105
+70 190
+70 382
+76 240
+77 272
+77 360
+77 544
+85 589
+87 31
+89 436
+92 7
+92 133
+97 354
+97 700
+98 403
+103 645
+108 381
+110 454
+112 58
+112 158
+112 550
+115 217
+118 621
+122 346
+123 407
+127 179
+128 483
+129 426
+130 81
+132 295
+132 676
+135 598
+136 566
+137 23
+140 259
+147 467
+150 701
+151 612
+153 377
+154 172
+154 217
+155 505
+157 58
+164 32
+164 248
+167 195
+167 680
+174 310
+179 163
+183 499
+188 260
+188 399
+188 548
+188 571
+191 5
+193 63
+193 379
+195 630
+196 523
+198 324
+202 239
+203 200
+204 217
+205 34
+208 452
+208 492
+223 434
+225 22
+225 270
+226 236
+226 476
+227 87
+228 635
+229 316
+230 167
+234 522
+234 541
+237 294
+237 612
+243 210
+243 676
+244 266
+245 119
+248 341
+257 571
+258 502
+259 142
+267 98
+269 6
+270 294
+271 533
+272 233
+273 694
+276 171
+277 353
+281 425
+282 330
+283 603
+286 642
+288 269
+288 372
+290 534
+293 199
+294 236
+298 104
+301 11
+303 465
+304 170
+306 669
+308 491
+314 232
+321 393
+323 192
+323 338
+324 574
+326 258
+329 654
+331 638
+332 3
+334 560
+335 414
+338 502
+339 26
+339 358
+341 132
+341 165
+342 239
+343 84
+343 527
+346 313
+357 497
+357 590
+360 52
+365 306
+365 612
+370 238
+370 698
+376 532
+377 56
+379 214
+381 136
+381 159
+384 178
+384 337
+390 15
+391 291
+391 456
+394 89
+396 636
+397 469
+398 256
+404 59
+405 678
+406 218
+410 402
+410 516
+415 4
+415 107
+417 81
+419 62
+419 147
+420 696
+424 306
+424 491
+426 589
+427 255
+429 34
+430 208
+435 542
+436 579
+436 631
+439 113
+441 344
+447 302
+448 50
+450 17
+450 156
+451 266
+451 515
+452 555
+453 381
+462 101
+462 122
+462 360
+462 477
+469 339
+470 178
+470 411
+471 202
+477 228
+477 317
+478 646
+479 49
+480 147
+480 436
+488 97
+488 202
+489 169
+492 451
+494 548
+494 673
+495 522
+498 609
+499 484
+503 282
+503 503
+504 245
+506 588
+508 47
+510 448
+515 569
+519 64
+522 660
+527 25
+529 303
+535 161
+535 445
+535 578
+536 343
+538 625
+539 660
+541 50
+541 233
+541 281
+542 512

Test_Images/IBA1_lowResolutionCH_2.txt

@@ -0,0 +1,17 @@
+AIDAhisto - Number of detected cells: 14
+cell postions (xy):
+
+4 127
+11 33
+16 131
+25 10
+30 93
+37 139
+50 149
+59 15
+74 112
+77 86
+82 18
+89 61
+113 45
+143 49

Test_Images/IBA1_lowResolutionCH_2_v.txt

@@ -0,0 +1,17 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells 14 
+x-y Cell Postitions 
+4 127
+11 33
+16 131
+25 10
+30 93
+37 139
+50 149
+59 15
+74 112
+77 86
+82 18
+89 61
+113 45
+143 49

Test_Images/IBA1_lowResolutionCH_3.txt

@@ -0,0 +1,167 @@
+AIDAhisto - Number of detected cells: 164
+cell postions (xy):
+
+3 79
+3 98
+4 118
+4 145
+5 69
+6 3
+6 25
+6 38
+7 129
+9 83
+9 122
+9 138
+10 9
+10 59
+12 39
+13 113
+14 35
+14 47
+15 106
+15 147
+16 62
+16 118
+18 79
+20 23
+20 121
+21 136
+22 63
+22 92
+25 19
+25 105
+26 81
+27 42
+27 72
+29 112
+29 146
+30 11
+30 49
+33 65
+33 96
+34 24
+35 2
+35 87
+36 140
+37 60
+37 123
+38 34
+39 107
+43 100
+44 56
+44 147
+45 9
+46 122
+47 72
+48 94
+48 131
+50 10
+51 115
+54 26
+54 51
+54 67
+55 104
+56 75
+56 85
+57 6
+57 19
+58 79
+58 142
+58 150
+62 4
+63 37
+64 64
+64 115
+65 25
+66 139
+67 19
+68 102
+69 2
+70 9
+70 118
+72 42
+72 112
+72 148
+73 55
+73 77
+76 116
+77 66
+77 125
+78 47
+78 88
+82 12
+83 69
+83 122
+83 139
+84 7
+84 21
+85 106
+89 131
+90 44
+91 90
+91 119
+92 56
+92 63
+93 16
+96 82
+96 143
+97 60
+98 76
+99 103
+102 31
+102 64
+102 95
+106 137
+107 149
+108 4
+108 39
+108 97
+109 73
+110 16
+110 118
+111 26
+112 131
+113 84
+114 5
+115 32
+116 147
+118 73
+118 80
+118 107
+118 113
+119 42
+123 21
+123 45
+123 94
+124 76
+125 119
+126 68
+126 105
+127 55
+129 15
+130 92
+130 147
+132 28
+132 37
+132 70
+134 49
+137 59
+138 99
+140 87
+142 12
+143 2
+144 51
+144 129
+145 74
+146 65
+147 46
+147 58
+148 39
+149 27
+149 140
+151 72
+151 148
+152 115
+155 128
+159 92

Test_Images/wholebrain_atlas.tif

@@ -0,0 +1 @@
+/annex/objects/MD5-s50118472--57796ecb719ea01f04b87d6bf3237b97

Test_Images/wholebrain_atlas2.tif

@@ -0,0 +1 @@
+/annex/objects/MD5-s50118461--49d89df95e00c68bf9bedfcfa9d540f7

Test_Images/wholebrain_atlas_splitted.tif

@@ -0,0 +1 @@
+/annex/objects/MD5-s50118461--49d89df95e00c68bf9bedfcfa9d540f7

Test_Images/wholebrain_slice.tif

@@ -0,0 +1 @@
+/annex/objects/MD5-s37589051--d56910758cd853f91331e893208ac9f0

Test_Images/wholebrain_slice.tif_process.log

@@ -0,0 +1 @@
+['/Volumes/AG_Aswendt_Share/Scratch/Shared_Software/Github/AIDAhisto_v1.1/testImages/wholebrain_slice.tif', '/Volumes/AG_Aswendt_Share/Scratch/Shared_Software/Github/AIDAhisto_v1.1/testImages/wholebrain_atlas.tif', '-o', '/Users/leon/Desktop/Software/AIDAhisto_v1.1_private']

Test_Images/wholebrain_sliceCH_1ROIs.txt

@@ -0,0 +1,97 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells in 94 given ROIs 
+
+2	SSp-m6b	28
+19	IG	5
+36	GU1	46
+72	ADP	0
+81	VL	63
+117	och	54
+120	AIp1	70
+129	V3	1
+148	GU4	14
+163	AIp2/3	25
+180	GU2/3	52
+187	GU5	10
+211	ACAd2/3	63
+226	LPO	5
+250	LSc	159
+258	LSr	307
+263	AVP	4
+272	AVPV	2
+296	ACAv2/3	72
+298	MA	10
+314	AIp6a	5
+320	MOp1	96
+342	SI	9
+344	AIp5	3
+351	BST	50
+450	SSp-ul1	81
+452	MEPO	1
+477	STR	162
+523	MPO	0
+558	SSp-n1	81
+564	MS	42
+577	SSp-ul4	119
+583	CLA	13
+588	ACAv1	115
+596	NDB	40
+625	SSp-ul5	206
+638	GU6a	8
+648	MOp5	719
+656	MOs1	101
+657	SSp-m2/3	80
+662	GU6b	0
+665	lot	21
+672	CP	3955
+698	OLF	42
+703	CTXsp	3
+754	OT	60
+763	OV	8
+767	MOs5	129
+772	ACAv5	48
+776	cc	1028
+803	PAL	50
+806	SSs2/3	97
+810	ACAv6a	46
+819	ACAv6b	12
+838	SSp-n2/3	182
+844	MOp6a	603
+849	VISC6b	0
+854	SSp-ul2/3	173
+857	VISC6a	8
+862	SSs6a	56
+873	SSs1	101
+878	SSp-m1	44
+882	MOp6b	140
+893	SSs6b	3
+897	VISC1	40
+900	aco	3
+908	act	0
+919	ACAd6a	13
+927	ACAd6b	1
+935	ACAd1	111
+940	cing	88
+943	MOp2/3	125
+945	SSp-ul6a	112
+950	SSp-m4	29
+952	EPd	29
+961	PIR	236
+962	MOs2/3	123
+974	SSp-m5	52
+985	MOp	35
+998	FS	9
+1009	fiber tracts	80
+1010	VISC4	23
+1015	ACAd5	47
+1021	MOs6a	47
+1026	SSp-ul6b	3
+1035	SSs4	22
+1058	VISC5	14
+1085	MOs6b	6
+1090	SSs5	34
+1097	HY	10
+1102	SSp-m6a	333
+1106	VISC2/3	28
+1109	PS	0
+182305696		6

Test_Images/wholebrain_slice_ch1_cC.tif

@@ -0,0 +1 @@
+/annex/objects/MD5-s12529843--c89554a715157d517e229082f55297cf

Test_Images/wholebrain_slice_ch1_cCMap.tif

@@ -0,0 +1 @@
+/annex/objects/MD5-s100236728--3dee990e245d87ff3305b0c3b1acbaeb

Test_Images/wholebrain_slice_ch1_cCROIs.txt

@@ -0,0 +1,96 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells in 94 given ROIs 
+
+2	SSp-m6b	74
+19	IG	10
+36	GU1	152
+72	ADP	4
+81	VL	111
+117	och	129
+120	AIp1	152
+129	V3	8
+148	GU4	49
+163	AIp2/3	98
+180	GU2/3	191
+187	GU5	34
+211	ACAd2/3	213
+226	LPO	16
+250	LSc	291
+258	LSr	871
+263	AVP	8
+272	AVPV	3
+296	ACAv2/3	229
+298	MA	43
+314	AIp6a	17
+320	MOp1	394
+342	SI	74
+344	AIp5	37
+351	BST	172
+450	SSp-ul1	236
+452	MEPO	6
+477	STR	473
+523	MPO	15
+558	SSp-n1	200
+564	MS	118
+577	SSp-ul4	271
+583	CLA	55
+588	ACAv1	246
+596	NDB	109
+625	SSp-ul5	421
+638	GU6a	42
+648	MOp5	1313
+656	MOs1	191
+657	SSp-m2/3	413
+662	GU6b	1
+665	lot	44
+672	CP	9526
+698	OLF	150
+703	CTXsp	11
+754	OT	240
+763	OV	17
+767	MOs5	281
+772	ACAv5	163
+776	cc	2190
+803	PAL	162
+806	SSs2/3	367
+810	ACAv6a	125
+819	ACAv6b	35
+838	SSp-n2/3	551
+844	MOp6a	1213
+849	VISC6b	2
+854	SSp-ul2/3	476
+857	VISC6a	52
+862	SSs6a	175
+873	SSs1	250
+878	SSp-m1	114
+882	MOp6b	282
+893	SSs6b	2
+897	VISC1	106
+900	aco	4
+908	act	0
+919	ACAd6a	57
+927	ACAd6b	7
+935	ACAd1	229
+940	cing	194
+943	MOp2/3	596
+945	SSp-ul6a	246
+950	SSp-m4	173
+952	EPd	104
+961	PIR	682
+962	MOs2/3	371
+974	SSp-m5	311
+985	MOp	103
+998	FS	35
+1009	fiber tracts	157
+1010	VISC4	89
+1015	ACAd5	183
+1021	MOs6a	135
+1026	SSp-ul6b	14
+1035	SSs4	126
+1058	VISC5	88
+1085	MOs6b	19
+1090	SSs5	188
+1097	HY	25
+1102	SSp-m6a	979
+1106	VISC2/3	119
+1109	PS	3

Test_Images/wholebrain_slice_ch1_intROIs.txt

@@ -0,0 +1,97 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain intensity 
+ Intensity in 94 given ROIs 
+Atlas region#
+2	462906
+19	38697
+36	1033865
+72	210331
+81	1076201
+117	1498906
+120	1516851
+129	84057
+148	408910
+163	1281663
+180	1230078
+187	477694
+211	1665647
+226	1755790
+250	2008652
+258	8257795
+263	410661
+272	150990
+296	1806302
+298	1712915
+314	310118
+320	2047314
+342	4440490
+344	884905
+351	3525886
+450	1697656
+452	376489
+477	5545748
+523	1553917
+558	1344638
+564	2205290
+577	2100801
+583	836217
+588	1861796
+596	1867452
+625	3258154
+638	704819
+648	14064960
+656	1263631
+657	3410336
+662	38114
+665	562624
+672	64986139
+698	1967582
+703	156998
+754	5795227
+763	254166
+767	2343065
+772	1396076
+776	13050835
+803	3307838
+806	3325702
+810	984164
+819	218169
+838	3486135
+844	9436578
+849	55399
+854	3615874
+857	551752
+862	1331547
+873	1897993
+878	723751
+882	2029731
+893	18593
+897	664750
+900	586688
+908	3659
+919	514647
+927	59449
+935	1561718
+940	1362368
+943	4748226
+945	1563595
+950	2990954
+952	1596003
+961	10114092
+962	2117266
+974	4501299
+985	1222911
+998	832840
+1009	1151251
+1010	596784
+1015	1701349
+1021	1034723
+1026	45400
+1035	1692277
+1058	886945
+1085	163961
+1090	2358564
+1097	757216
+1102	7295854
+1106	822378
+1109	166459
+182305696	148876

Test_Images/wholebrain_slice_ch3_cC.tif

@@ -0,0 +1 @@
+/annex/objects/MD5-s12529677--1a706d4a9e78db8f9eed7b12d6762f81

Test_Images/wholebrain_slice_ch3_cCROIs.txt

@@ -0,0 +1,96 @@
+Number of detected cells in 94 given ROIs
+
+2	117
+19	6
+36	149
+72	94
+81	120
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Test_Images_SC/SP_V1_10_4_slide30_DAPI_mergeCH_1ROIs.txt

@@ -0,0 +1,65 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells in 62 given ROIs 
+
+4	1Sp 	82
+9	5SpL 	136
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+715	Ax9 	14
+720	2SpO 	103
+729	7Sp 	584
+740	IB 	30
+744	Rh9 	37

Test_Images_SC/SP_V1_10_4_slide30_GFAP_merge.tif

@@ -0,0 +1 @@
+/annex/objects/MD5-s21886191--49f1392dd01a73ad0da64dc3c0c520e8

Test_Images_SC/SP_V1_10_4_slide30_GFAP_mergeCH_1ROIs.txt

@@ -0,0 +1,65 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells in 62 given ROIs 
+
+4	1Sp 	121
+9	5SpL 	48
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+715	Ax9 	6
+720	2SpO 	117
+729	7Sp 	173
+740	IB 	5
+744	Rh9 	26

Test_Images_SC/SP_V1_10_4_slide30_GFAP_mergeCH_1ROIs_v.txt

@@ -0,0 +1,65 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells in 62 given ROIs 
+
+4	1Sp 	65
+9	5SpL 	28
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+715	Ax9 	4
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+729	7Sp 	93
+740	IB 	5
+744	Rh9 	14

Test_Images_SC/SP_V1_10_4_slide30_Iba1_mergeCH_1ROIs.txt

@@ -0,0 +1,65 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells in 62 given ROIs 
+
+4	1Sp 	17
+9	5SpL 	24
+19	2SpI 	28
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+30	SI9 	5
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+250		2
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+709	rs 	23
+715	Ax9 	4
+720	2SpO 	39
+729	7Sp 	114
+740	IB 	3
+744	Rh9 	8

Test_Images_SC/SP_V1_10_4_slide30_Iba1_mergeCH_1ROIs_v.txt

@@ -0,0 +1,65 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells in 62 given ROIs 
+
+4	1Sp 	12
+9	5SpL 	13
+19	2SpI 	14
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+30	SI9 	2
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Test_Images_SC/SP_V1_10_4_slide30_SMI32_mergeCH_1ROIs.txt

@@ -0,0 +1,65 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells in 62 given ROIs 
+
+4	1Sp 	0
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+715	Ax9 	6
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+729	7Sp 	289
+740	IB 	5
+744	Rh9 	23

Test_Images_SC/SP_V1_10_4_slide30_SMI32_mergeCH_1ROIs_v.txt

@@ -0,0 +1,65 @@
+AIDAhisto: Atlas-based imaging data analysis tool for mouse brain histology 
+Number of identified Cells in 62 given ROIs 
+
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Test_Images_SC/TransformedAtlas_C5.tif

@@ -0,0 +1 @@
+/annex/objects/MD5-s29181540--7157bb1a16b40295f28152fc6ce85eae