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<p>Dear Zongli,</p>
<p>I hope you are well.</p>
<p>I have also seen this issue when GMS crashes. For some reason
after the crash, the compression of the TIFF will add some extra
pixel rows and columns to all the TIFFS. The manner in which they
are added are around the perimeter of each frame. So if we have a
row with 7676, row 0 and 1 will have the extra pixels and row 7679
and 7680 will also have extra pixels. In the other direction for
7420, column 0 and 1 will have the extra pixels and column 7423
and 7424 will have the extra pixels. It is as if there is a 2pixel
wide "picture frame" around the image. <br>
</p>
<p>I have found that it would be more labor intensive to clip each
TIFF so instead I would add pixels to the gain reference in order
to make it the same dimensions as the "corrupt" movies. Making the
gain reference 7680x7424 will allow it to be compatible with the
movies and MotionCorr will not complain that the gain reference is
a different size. <br>
</p>
<p>One last thing is that in order to make this problem go away you
must close serial EM, DM, and power cycle the K2 camera, digitizer
and processor. Hope it works.<br>
</p>
<p>Best,</p>
<p>Mark</p>
<p><a class="moz-txt-link-abbreviated" href="http://www.subangstrom.com">www.subangstrom.com</a><br>
</p>
<br>
<div class="moz-cite-prefix">On 8/29/2018 10:12 PM, Zongli Li wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAPWpDO1qHeVa3DM5QdXzWafnSt=CYMj0MpTL9Y8qaJDD84s-Vg@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<div dir="ltr">Dear lists,
<div>
<p
style="color:rgb(0,0,0);margin-top:0px;margin-bottom:0px;font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont">Due
to an error from Gatan GMS, half of my data set have a wrong
image size (7680x7424). The correct image size and the gain
reference image is 7676x7420. </p>
<p
style="color:rgb(0,0,0);margin-top:0px;margin-bottom:0px;font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont">The
image stack were collected on K2 camera set at super
resolution, using SerialEM and set to dark gain subtracted
and LZW compression.<br>
</p>
<p
style="color:rgb(0,0,0);margin-top:0px;margin-bottom:0px;font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont">I
would like to clip the tif stack to 7676x7420 so it matches
the size of the gain reference image. What is the correct
way to clip the tif stack? (which pixels should be cut off)</p>
<p
style="color:rgb(0,0,0);margin-top:0px;margin-bottom:0px;font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont"><br>
</p>
<p
style="color:rgb(0,0,0);margin-top:0px;margin-bottom:0px;font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont">Thanks
in advance,</p>
<p
style="color:rgb(0,0,0);margin-top:0px;margin-bottom:0px;font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont"><br>
</p>
<p
style="color:rgb(0,0,0);margin-top:0px;margin-bottom:0px;font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont">Zongli</p>
<p
style="color:rgb(0,0,0);font-size:16px;margin-top:0px;margin-bottom:0px;font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont"><br>
</p>
<br class="gmail-Apple-interchange-newline"
style="color:rgb(0,0,0);font-family:-webkit-standard">
</div>
</div>
<br>
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