Installation on the microscope computer » History » Version 1
Amber Herold, 04/14/2010 02:51 PM
1 | 1 | Amber Herold | h1. Additional installation on the microscope computer |
---|---|---|---|
2 | |||
3 | |||
4 | |||
5 | |||
6 | |||
7 | The full leginon and its supporting packages need to be installed on the Windows computer |
||
8 | controlling the microscope. Additional programs are required for communication with the CCD |
||
9 | and extra functions for Tecnai scripting not supported as default by FEI Tecnai |
||
10 | microscopes |
||
11 | |||
12 | |||
13 | |||
14 | h2. Required supporting programs for the CCD camera from camera makers |
||
15 | |||
16 | |||
17 | |||
18 | Install and register the following programs for CCD cameras from the two makes: |
||
19 | |||
20 | |||
21 | |||
22 | |_.Camera Make:|_.File:| |
||
23 | | Gatan|TecnaiCCD.dll| |
||
24 | | Tietz|CAMC4.exe*| |
||
25 | |||
26 | |||
27 | |||
28 | |||
29 | * We have experienced slowness of the CAMC4.exe comes with later version Tecnai TUI/TIA. |
||
30 | Replacing it with an earlier version of CAMC4.exe resolved the problem. |
||
31 | |||
32 | |||
33 | |||
34 | |||
35 | |||
36 | h2. Additional Package required from NRAMM for Gatan camera or camera that uses TIA |
||
37 | |||
38 | |||
39 | |||
40 | For Gatan Camera or FEI Eagle Camera that uses TIA, comarray package need to be install |
||
41 | with python |
||
42 | |||
43 | |||
44 | |||
45 | |_.SVN Package Name|_.Installed Python Package Name|_.Reason for update:| |
||
46 | |comarray|comarray|com module output conversion to array| |
||
47 | |||
48 | |||
49 | |||
50 | |||
51 | |||
52 | |||
53 | * <link linkend="window_svn">Check out the comarray package</link> from svn |
||
54 | depository with your SVN client |
||
55 | |||
56 | <pre>cd Leginon-1.6-ALL |
||
57 | svn co http://emg.nysbc.org/svn/comarray/branches/leg1.6 comarray</pre> |
||
58 | |||
59 | * Start a command line Window from Start Menu |
||
60 | |||
61 | |||
62 | * Install the package with commands such as |
||
63 | <pre>cd Your_Download_Place\Leginon-1.6-ALL\comarray |
||
64 | c:\\python25\python.exe setup.py install</pre> |
||
65 | |||
66 | |||
67 | |||
68 | |||
69 | |||
70 | |||
71 | |||
72 | |||
73 | |||
74 | h2. Supporting programs for film exposure |
||
75 | |||
76 | |||
77 | |||
78 | Install the following if you need film exposure on FEI Tecnai TEM through Leginon, |
||
79 | available through FEI. Please contact Max Otten: <email>mto@feico.com</email> and request |
||
80 | for adaexp.exe that works with your version of Tecnai user interface program. |
||
81 | |||
82 | |||
83 | |||
84 | |_.Name:|_.File:| |
||
85 | | exposure adaptor|adaexp.exe| |
||
86 | |||
87 | |||
88 | |||
89 | |||
90 | |||
91 | |||
92 | |||
93 | h2. Register adaexep.exe |
||
94 | |||
95 | |||
96 | |||
97 | * From the command prompt: |
||
98 | |||
99 | <pre>adaexp.exe /regserver</pre> |
||
100 | |||
101 | * From the program start menu under pyScope or |
||
102 | C:\Python25\Lib\site-packages\pyScope\ |
||
103 | |||
104 | <pre>updatecom.py</pre> |
||
105 | |||
106 | |||
107 | |||
108 | |||
109 | |||
110 | |||
111 | |||
112 | |||
113 | h2. Modify instruments.cfg: |
||
114 | |||
115 | |||
116 | |||
117 | Sinedon now have full control of database interaction, therefore, the database |
||
118 | configuration in leginon.cfg is no longer needed. |
||
119 | |||
120 | |||
121 | |||
122 | |||
123 | * Modify the file instruments.cfg in the installed pyScope directory to that for |
||
124 | your microscope and camera. For example, if your microscope uses Tecnai Scripting |
||
125 | Interface and you have a Gatan camera that you interface through |
||
126 | DigitalMicrograph: |
||
127 | |||
128 | |||
129 | |||
130 | <pre>[tem] |
||
131 | class: tecnai.Tecnai |
||
132 | [camera] |
||
133 | class: gatan.Gatan</pre> |
||
134 | |||
135 | |||
136 | |||
137 | The file contains other examples of microscope and camera drivers that we |
||
138 | distribute from NRAMM. |
||
139 | |||
140 | |||
141 | |||
142 | |||
143 | |||
144 | |||
145 | |||
146 | |||
147 | |||
148 | h2. Run updatecom.py |
||
149 | |||
150 | |||
151 | |||
152 | From a command line window: |
||
153 | |||
154 | |||
155 | |||
156 | <pre>cd C:\python25\Lib\Site-Packages\pyScope |
||
157 | C:\python25\python.exe updatecom.py</pre> |
||
158 | |||
159 | |||
160 | |||
161 | This should generate a few files, including tecnaicom.py, gatancom.py and tietzcom.py, |
||
162 | in the same directory. |
||
163 | |||
164 | |||
165 | |||
166 | |||
167 | |||
168 | h2. Additional setup on Tietz PXL camera (optional) |
||
169 | |||
170 | |||
171 | |||
172 | The actual Tietz PXL camera dimension is slightly larger than 2048 x 2048. If you'd like |
||
173 | to take the images using the maximum of 2048 x 2048 pixels, you may modify the function that |
||
174 | get camera dimension in tietz.py of pyScope package. |
||
175 | |||
176 | |||
177 | * Go to C:\Python25\Lib\site-packages\pyScope\ |
||
178 | |||
179 | |||
180 | * Edit tietz.py with a plain text editor |
||
181 | |||
182 | |||
183 | * Find the lines: |
||
184 | |||
185 | |||
186 | |||
187 | <pre> def getCameraSize(self): |
||
188 | # {'type': dict, 'values': {'x': {'type': int}, 'y': {'type': int}}}} |
||
189 | x = self._getParameterValue('cpTotalDimensionX') |
||
190 | y = self._getParameterValue('cpTotalDimensionY') |
||
191 | return {'x': x, 'y': y} |
||
192 | </pre> |
||
193 | |||
194 | |||
195 | |||
196 | * Change the last line to: |
||
197 | |||
198 | |||
199 | |||
200 | <pre> return {'x': 2048, 'y': 2048}</pre> |
||
201 | |||
202 | |||
203 | |||
204 | |||
205 | |||
206 | |||
207 | |||
208 | |||
209 | h2. Additional Software (Optional): |
||
210 | |||
211 | |||
212 | TightVNC (http://www.tightvnc.com) if you get tired of going into the microscope room |
||
213 | just to open the column valves. |