-
Notifications
You must be signed in to change notification settings - Fork 0
/
2_Image_Batch_Registration.ijm
293 lines (281 loc) · 10.2 KB
/
2_Image_Batch_Registration.ijm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
s=File.separator
Dialog.create("Bruker Data Manager");
Dialog.addCheckbox("Input Directory = Output Directory", true);
Dialog.addMessage("Image Registration (1 Channel Images):");
Dialog.addCheckbox("Single Channel Image Registration", false);
Dialog.addMessage("Image Registration (2 Channel Images):");
Dialog.addCheckbox("Ch2 (Green) Only Registration", false);
Dialog.addCheckbox("Ch1 (Red) Only Registration", false);
Dialog.addCheckbox("Ch2 to Ch1 Channel Registration", false);
Dialog.addCheckbox("Ch1 to Ch2 Channel Registration", false);
items = newArray("AVG Complete", "AVG Selection");
Dialog.addRadioButtonGroup("", items, 1, 2, "AVG Complete");
Dialog.addSlider("Start Slice", 1, 9999, 1);
Dialog.addSlider("Stop Slice", 1, 9999, 9999);
Dialog.show();
inDisOutD=Dialog.getCheckbox();
SChReg=Dialog.getCheckbox();
GReg=Dialog.getCheckbox();
RReg=Dialog.getCheckbox();
C2toC1=Dialog.getCheckbox();
C1toC2=Dialog.getCheckbox();
AVG=Dialog.getRadioButton();
AVGStart=Dialog.getNumber();
AVGStop=Dialog.getNumber();
inDir=getDirectory("Choose the Raw Data Containing Folder");
if (inDisOutD==true) {
outDir=inDir;
}
else {
outDir=getDirectory("Choose Output Folder");
if ((inDir==outDir) || (startsWith(outDir, inDir))) {
exit("Input folder must be different from and not within output folder!");
}
}
setBatchMode(true);
if (SChReg==true) {
SingleChannelImageRegistration(inDir, outDir);
}
if (GReg==true) {
source1="C2";
source2="C1";
target1="C2";
target2="C1";
RegisterFilesChannelABOnly(inDir, outDir);
}
if (RReg==true) {
source1="C1";
source2="C2";
target1="C1";
target2="C2";
RegisterFilesChannelABOnly(inDir, outDir);
}
if (C2toC1==true) {
source1="C1";
source2="C2";
target1="C1";
target2="C2";
RegisterFilesChannelAToChannelB(inDir, outDir);
}
if (C1toC2==true) {
source1="C2";
source2="C1";
target1="C2";
target2="C1";
RegisterFilesChannelAToChannelB(inDir, outDir);
}
print("Done");
setBatchMode(false);
function SingleChannelImageRegistration(inDir, outDir) {
list = getFileList(inDir);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/")) {
DuplicatePath=replace(inDir+s+list[i], inDir, outDir);
if (!File.exists(DuplicatePath)) {
File.makeDirectory(DuplicatePath);
}
SingleChannelImageRegistration(inDir+list[i],outDir+list[i]);
}
else if ((endsWith(list[i], "_Stack_Extr.tif"))&&(!File.exists(replace(outDir+s+list[i],"_Stack_Extr.tif", "_SReg.tif")))) {
DestinationFilePath=replace(inDir+s+list[i], inDir, outDir);
open(inDir+list[i]);
name=File.getName(inDir+list[i]);
selectWindow(name);
width=getWidth();
height=getHeight();
rename("source");
if (AVG=="AVG Complete") {
run("Z Project...", "projection=[Average Intensity]");
}
else if (AVG=="AVG Selection") {
run("Z Project...", "start="+AVGStart+" stop="+AVGStop+" projection=[Average Intensity]");
}
selectWindow("AVG_source");
rename("target");
selectWindow("source");
sln=nSlices;
for(k=1; k <=sln; k++) {
selectWindow("source");
setSlice(k);
run("Duplicate...", "title=currentFrame");
run("TurboReg ", "-align -window currentFrame 0 0 "+(width - 1)+" " +(height - 1)+" "+"-window target 0 0 "+(width - 1)+" "+(height - 1)+" -rigidBody "+(width / 2)+" "+(height / 2)+" "+(width / 2)+" "+(height / 2)+" "+"0 " + (height / 2)+" 0 "+(height / 2)+" "+(width - 1)+" "+(height / 2)+" "+(width - 1)+" "+(height / 2)+" -showOutput");
selectWindow("Output");
rename("outputimg");
run("Duplicate...", "title=registered");
if(k==1) {
run("Duplicate...", "title=" + "regstack");
selectWindow("registered");
close();
}
else {
run("Concatenate...", " title=" + "regstack" + " image1=" + "regstack" + " image2=registered image3=[-- None --] image4=[-- None --]");
}
selectWindow("outputimg");
close();
selectWindow("currentFrame");
close();
}
selectWindow("regstack");
run("16-bit");
saveAs("tiff", replace(DestinationFilePath, "_Stack_Extr.tif", "_SReg.tif"));
run("Close All");
close("Refined Landmarks");
run("Collect Garbage");
close("Log");
}
}
}
function RegisterFilesChannelABOnly(inDir, outDir) {
list = getFileList(inDir);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/")) {
DuplicatePath=replace(inDir+s+list[i], inDir, outDir);
if (!File.exists(DuplicatePath)) {
File.makeDirectory(DuplicatePath);
}
RegisterFilesChannelABOnly(inDir+list[i],outDir+list[i]);
}
else if ((endsWith(list[i], "_Stack_Extr.tif"))&&(!File.exists(replace(outDir+s+list[i],"_Stack_Extr.tif", "_"+source1+"_Reg.tif")))) {
DestinationFilePath=replace(inDir+s+list[i], inDir, outDir);
open(inDir+list[i]);
name=File.getName(inDir+list[i]);
selectWindow(name);
width=getWidth();
height=getHeight();
rename("source");
if (AVG=="AVG Complete") {
run("Z Project...", "projection=[Average Intensity]");
}
else if (AVG=="AVG Selection") {
run("Z Project...", "start="+AVGStart+" stop="+AVGStop+" projection=[Average Intensity]");
}
selectWindow("AVG_source");
rename("target");
run("Split Channels");
close(target2+"-target");
selectWindow("source");
run("Split Channels");
sln=nSlices;
close(source2+"-source");
for(k=1; k <=sln; k++) {
selectWindow(source1+"-source");
setSlice(k);
run("Duplicate...", "title=currentFrame");
run("TurboReg ", "-align "+"-window currentFrame 0 0 "+(width - 1)+" " +(height - 1)+" "+"-window "+target1+"-target 0 0 "+(width - 1)+" "+(height - 1) +" -rigidBody "+(width / 2)+" "+(height / 2)+" "+ (width / 2) + " " + (height / 2) + " "+ "0 " + (height / 2) + " 0 "+(height / 2)+" "+(width - 1)+" "+(height / 2)+" "+(width - 1)+" "+(height / 2)+" -showOutput");
selectWindow("Output");
rename("outputimg");
run("Duplicate...", "title=registered");
if(k==1) {
run("Duplicate...", "title=" + "regstack");
selectWindow("registered");
close();
}
else {
run("Concatenate...", " title=" + "regstack" + " image1=" + "regstack" + " image2=registered image3=[-- None --] image4=[-- None --]");
}
selectWindow("outputimg");
close();
selectWindow("currentFrame");
close();
}
selectWindow("regstack");
resetMinAndMax();
run("16-bit");
saveAs("tiff", replace(DestinationFilePath, "_Stack_Extr.tif", "_"+source1+"_Reg.tif"));
run("Close All");
close("Refined Landmarks");
run("Collect Garbage");
close("Log");
}
}
}
function RegisterFilesChannelAToChannelB(inDir, outDir) {
list = getFileList(inDir);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/")) {
DuplicatePath=replace(inDir+s+list[i], inDir, outDir);
if (!File.exists(DuplicatePath)) {
File.makeDirectory(DuplicatePath);
}
RegisterFilesChannelAToChannelB(inDir+list[i],outDir+list[i]);
}
else if ((endsWith(list[i], "_Stack_Extr.tif"))&&(!File.exists(replace(outDir+s+list[i],"_Stack_Extr.tif", "_"+source2+"to"+source1+"_Reg.tif")))) {
DestinationFilePath=replace(inDir+s+list[i], inDir, outDir);
open(inDir+list[i]);
name=File.getName(inDir+list[i]);
selectWindow(name);
width=getWidth();
height=getHeight();
rename("source");
if (AVG=="AVG Complete") {
run("Z Project...", "projection=[Average Intensity]");
}
else if (AVG=="AVG Selection") {
run("Z Project...", "start="+AVGStart+" stop="+AVGStop+" projection=[Average Intensity]");
}
selectWindow("AVG_source");
rename("target");
run("Split Channels");
close(target2+"-target");
selectWindow("source");
run("Split Channels");
sln=nSlices;
for(k=1; k <=sln; k++) {
selectWindow(source1+"-source");
run("Duplicate...", "title="+source1+"-currentFrame duplicate range="+k+"");
selectWindow(source2+"-source");
run("Duplicate...", "title="+source2+"-currentFrame duplicate range="+k+"");
run("TurboReg ", "-align "+"-window "+source1+"-currentFrame 0 0 "+(width - 1)+" " +(height - 1)+" "+"-window "+target1+"-target 0 0 "+(width - 1)+" "+(height - 1) +" -rigidBody "+(width / 2)+" "+(height / 2)+" "+ (width / 2) + " " + (height / 2) + " "+ "0 " + (height / 2) + " 0 "+(height / 2)+" "+(width - 1)+" "+(height / 2)+" "+(width - 1)+" "+(height / 2)+" -showOutput");
SX1=getResult("sourceX", 0);
SY1=getResult("sourceY", 0);
TX1=getResult("targetX", 0);
TY1=getResult("targetY", 0);
SX2=getResult("sourceX", 1);
SY2=getResult("sourceY", 1);
TX2=getResult("targetX", 1);
TY2=getResult("targetY", 1);
SX3=getResult("sourceX", 2);
SY3=getResult("sourceY", 2);
TX3=getResult("targetX", 2);
TY3=getResult("targetY", 2);
selectWindow("Output");
resetMinAndMax();
run("Duplicate...", "title="+source1+"-registered");
close("Output");
run("TurboReg ", "-transform -window "+source2+"-currentFrame "+(width)+" "+(height)+" -rigidBody "+SX1+" "+SY1+" "+TX1+ " "+TY1+" "+SX2+" "+SY2+" "+TX2+" "+TY2+" "+SX3+" "+SY3+" "+TX3+" "+TY3+" -showOutput");
selectWindow("Output");
resetMinAndMax();
run("Duplicate...", "title="+source2+"-registered");
close("Output");
if(k==1) {
selectWindow(source2+"-registered");
run("Duplicate...", "title="+source2+"-regstack");
selectWindow(source1+"-registered");
run("Duplicate...", "title="+source1+"-regstack");
close(source2+"-registered");
close(source1+"-registered");
}
else {
run("Concatenate...", " title="+source2+"-regstack" + " image1="+source2+"-regstack" + " image2="+source2+"-registered image3=[-- None --] image4=[-- None --]");
run("Concatenate...", " title="+source1+"-regstack" + " image1="+source1+"-regstack" + " image2="+source1+"-registered image3=[-- None --] image4=[-- None --]");
}
close(source1+"-currentFrame");
close(source2+"-currentFrame");
close(source1+"-registered");
close(source2+"-registered");
}
run("Merge Channels...", "c1=C1-regstack c2=C2-regstack create");
selectWindow("regstack");
Stack.setDisplayMode("grayscale");
Stack.setChannel(1);
resetMinAndMax();
Stack.setChannel(2);
resetMinAndMax();
saveAs("tiff", replace(DestinationFilePath, "_Stack_Extr.tif", "_"+source2+"to"+source1+"_Reg.tif"));
run("Close All");
close("Refined Landmarks");
run("Collect Garbage");
close("Log");
}
}
}