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<div class="moz-cite-prefix">Dear All,<br>
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<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">Steve Ludke (and others)
are right: the best thing to do is
to store the integer counting files for compact long-term
storage, and do any
“gain correction” later, prior to processing. Movies collected
in counting mode
is what the discussion is about here! However, gain correction
(as per the
camera manufacture’s procedures) are always sub-optimal and I
prefer to speak of
“camera normalization” (see below), but let us start at the
beginning: </span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">(1) The IMAGIC format, from
its early beginnings<span style="mso-spacerun:yes"> </span>[van
Heel & Keegstra 1981], was designed
for handling large sets of images (“stacks”) with each image
in the stack
(stored in the “.IMG” file) having its own header (stored in a
separate ‘.HED’
file). The same format also allows for multidimensional data,
say stacks of 3D
volumes, or stacks of thousands of movies, each containing,
say 128 frames. The
files can be huge (~terabytes) but fast random access of all
images is
guaranteed by all images having the same size, giving
predictability of where
each one starts. The stack approach has since proliferated to
other systems
like SPIDER and MRC, but only as an add-on and never as the
core of the system,
expecting all programs by default to conveniently loop over
all images or 3Ds
in the stack. Compressing an IMAGIC image stack containing a
huge set of movies, is
trivial and very effective using standard ZIP-type
compressors. </span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">(2) The MRC format
[Crowther 1996] is a derivative of the
earlier CCP4 format for 3D X-ray volume data. The MRC format
is not optimized
for storing many 2D images since it only supports ONE image
and ONE header encoded
in ONE file. Because of the limitations of the MRC format many
variants and
extensions have been introduced for specific purposes by many
different researchers that are difficult to
keep track of leading to incompatibilities. <span
style="mso-spacerun:yes"> </span>The extension of the MRC
format to store a large number of individual images (stacks)
is primitive
while all images share the same header. The MRC stack was
adopted by some for
storing cryo-EM movies. The individual frame images contain a
low number of electron
counts, implying that most of the bits in the movie are “0”
and thus the movie can
easily be compressed to a minimal size by any standard “ZIP”
program.</span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">(3) The TIFF (= Tagged
Image File Format) is a popular
format in its simplest form, but complicated and not universal
in all its
extensions. Many variants with specific TAGs exist that make
no sense outside a
given application. TIFFs exist that can hold multiple images
(stacks) but don’t
count on standard imaging programs being able to look at
anything more than the
first image in the stack. <span style="mso-spacerun:yes"> </span>The
enthusiasm
Steve and others expressed reflects only the storing a stack
of 8-bits/pixel
movies stored in TIFF compressed mode, exploiting loss-less
compression options
available in standard libraries.<span style="mso-spacerun:yes">
</span>However,
having hundreds or thousands of such individual TIFF movies
floating around in
a single directory is as chaotic as is having hundreds or
thousands of MRCs
movie files in a directory. The ZIP compression will actually
allow you to organize such an overall mess a bit better into a
single sub-directory/file.</span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">(4) Data compression of a
stack of images (loss-less)
makes that each compressed image has a different size and that
thus each image
begins at an unpredictable point in the file (see (2) above).
<span style="mso-spacerun:yes"> </span>For random access to
the compressed images
this requires an additional level of organization/complexity
which may even
require reading/decompressing the whole file in the computer
memory. So far, I
have preferred to loss-less compress raw counting images (MRCs
or IMAGIC byte
format or…) separate from any real data processing.</span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">(5) The Camera
manufacturer’s “gain corrections” are
normally sub-optimal and our “camera normalization” based on
the collected data sets can considerably improve the data set
even after an a-priori standard gain
correction [Afanasyev 2015 Sci. Rep.].<span
style="mso-spacerun:yes"> </span>The
floating-point images needed for correction are the average
image and the
standard deviation image of a large data set and these are
normally derived from
the data set itself. The camera normalization will remove
spurious correlations
between images (say, movie frames) and will thus, for example,
allow better
movie alignments, based on smaller subareas of the movies. We
have not yet seen
a case where the manufacturers gain correction could not be
improved upon based
on the spurious correlations between the corrected images
measured by FRC [Afanasyev
2015]. The a-posteriori camera correction can, in fact,
replace the manufactures
gain correction in many/most cases.</span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">(6) Finally, for a better
understanding of the
fundamentals, let us reverse the thinking and perform what
theoretically would be the best possible
data collection experiment: Let us register the arrival of
each individual
electron of a movie! Each electron hits somewhere on a 4kx4k
chip (= 2**12 x
2**12 = 2**24 pixels possible), arriving in one of the 128
movie frames (= 2**7
possibilities) to achieve an average accumulated dose per
pixel of ~64
electrons (= 2**6). The size of such an ideal data set of
individual electron
arrivals would thus be:<span style="mso-spacerun:yes"> </span>~2**(12+12+7+6)
= 2**37 bits; or, ~512 Mbyte. Had you measured your 128 movie
frames at the byte level (16Mbyte/frame), you would have ended
up with a movie
of ~2 Tbyte. <span style="mso-spacerun:yes"> </span>Thus, by
counting the
arrival of the individual electrons, you have achieved a
“compression rate” of
75%. However, if you would already have been satisfied with an
average count of
only 16 electrons per pixel, your ideal collected movie data
set would have
shrunk to 128 Mbyte and, everything else being the same, your
“loss-less compression
rate” would have been 94%! What I am trying to say here is
that those compression
rates are NOT a virtue of your favorite compression algorithm
but are due to the intrinsic redundancies of your movie data!</span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">Bottom lines: <span
style="mso-spacerun:yes"></span>(A)
Use loss-less compression of your counting files and store
them forever! (B) The
on-the-fly loss-less compression of floating-point images
probably causes more problems
than the limited saving of space is worth. (C) Since in
cryo-EM the noise is the
carrier of the information, stay away from any compression
algorithm that is
not loss-less: it may kill your information!! (D) Loss-less
compression of huge
stacks of final-results floating-point data sets will probably
also save you a significant
amount of space (in the order of 10-40%).</span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">My few cents (may save you
thousands… ;) ).</span></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;line-height:107%;font-family:
"Times New Roman",serif">Marin </span></p>
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Name="envelope return"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="footnote reference"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="annotation reference"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="line number"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="page number"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="endnote reference"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="endnote text"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="table of authorities"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="macro"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="toa heading"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Bullet"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Number"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List 4"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List 5"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Bullet 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Bullet 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Bullet 4"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Bullet 5"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Number 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Number 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Number 4"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Number 5"/>
<w:LsdException Locked="false" Priority="10" QFormat="true" Name="Title"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Closing"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Signature"/>
<w:LsdException Locked="false" Priority="1" SemiHidden="true"
UnhideWhenUsed="true" Name="Default Paragraph Font"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Body Text"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Body Text Indent"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Continue"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Continue 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Continue 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Continue 4"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="List Continue 5"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Message Header"/>
<w:LsdException Locked="false" Priority="11" QFormat="true" Name="Subtitle"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Salutation"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Date"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Body Text First Indent"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Body Text First Indent 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Note Heading"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Body Text 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Body Text 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Body Text Indent 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Body Text Indent 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Block Text"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Hyperlink"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="FollowedHyperlink"/>
<w:LsdException Locked="false" Priority="22" QFormat="true" Name="Strong"/>
<w:LsdException Locked="false" Priority="20" QFormat="true" Name="Emphasis"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Document Map"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Plain Text"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="E-mail Signature"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Top of Form"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Bottom of Form"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Normal (Web)"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Acronym"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Address"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Cite"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Code"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Definition"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Keyboard"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Preformatted"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Sample"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Typewriter"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="HTML Variable"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Normal Table"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="annotation subject"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="No List"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Outline List 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Outline List 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Outline List 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Simple 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Simple 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Simple 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Classic 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Classic 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Classic 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Classic 4"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Colorful 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Colorful 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Colorful 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Columns 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Columns 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Columns 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Columns 4"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Columns 5"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Grid 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Grid 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Grid 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Grid 4"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Grid 5"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Grid 6"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Grid 7"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Grid 8"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table List 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table List 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table List 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table List 4"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table List 5"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table List 6"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table List 7"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table List 8"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table 3D effects 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table 3D effects 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table 3D effects 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Contemporary"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Elegant"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Professional"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Subtle 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Subtle 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Web 1"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Web 2"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Web 3"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Balloon Text"/>
<w:LsdException Locked="false" Priority="39" Name="Table Grid"/>
<w:LsdException Locked="false" SemiHidden="true" UnhideWhenUsed="true"
Name="Table Theme"/>
<w:LsdException Locked="false" SemiHidden="true" Name="Placeholder Text"/>
<w:LsdException Locked="false" Priority="1" QFormat="true" Name="No Spacing"/>
<w:LsdException Locked="false" Priority="60" Name="Light Shading"/>
<w:LsdException Locked="false" Priority="61" Name="Light List"/>
<w:LsdException Locked="false" Priority="62" Name="Light Grid"/>
<w:LsdException Locked="false" Priority="63" Name="Medium Shading 1"/>
<w:LsdException Locked="false" Priority="64" Name="Medium Shading 2"/>
<w:LsdException Locked="false" Priority="65" Name="Medium List 1"/>
<w:LsdException Locked="false" Priority="66" Name="Medium List 2"/>
<w:LsdException Locked="false" Priority="67" Name="Medium Grid 1"/>
<w:LsdException Locked="false" Priority="68" Name="Medium Grid 2"/>
<w:LsdException Locked="false" Priority="69" Name="Medium Grid 3"/>
<w:LsdException Locked="false" Priority="70" Name="Dark List"/>
<w:LsdException Locked="false" Priority="71" Name="Colorful Shading"/>
<w:LsdException Locked="false" Priority="72" Name="Colorful List"/>
<w:LsdException Locked="false" Priority="73" Name="Colorful Grid"/>
<w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 1"/>
<w:LsdException Locked="false" Priority="61" Name="Light List Accent 1"/>
<w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 1"/>
<w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 1"/>
<w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 1"/>
<w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 1"/>
<w:LsdException Locked="false" SemiHidden="true" Name="Revision"/>
<w:LsdException Locked="false" Priority="34" QFormat="true"
Name="List Paragraph"/>
<w:LsdException Locked="false" Priority="29" QFormat="true" Name="Quote"/>
<w:LsdException Locked="false" Priority="30" QFormat="true"
Name="Intense Quote"/>
<w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 1"/>
<w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 1"/>
<w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 1"/>
<w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 1"/>
<w:LsdException Locked="false" Priority="70" Name="Dark List Accent 1"/>
<w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 1"/>
<w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 1"/>
<w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 1"/>
<w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 2"/>
<w:LsdException Locked="false" Priority="61" Name="Light List Accent 2"/>
<w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 2"/>
<w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 2"/>
<w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 2"/>
<w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 2"/>
<w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 2"/>
<w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 2"/>
<w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 2"/>
<w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 2"/>
<w:LsdException Locked="false" Priority="70" Name="Dark List Accent 2"/>
<w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 2"/>
<w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 2"/>
<w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 2"/>
<w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 3"/>
<w:LsdException Locked="false" Priority="61" Name="Light List Accent 3"/>
<w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 3"/>
<w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 3"/>
<w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 3"/>
<w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 3"/>
<w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 3"/>
<w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 3"/>
<w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 3"/>
<w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 3"/>
<w:LsdException Locked="false" Priority="70" Name="Dark List Accent 3"/>
<w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 3"/>
<w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 3"/>
<w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 3"/>
<w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 4"/>
<w:LsdException Locked="false" Priority="61" Name="Light List Accent 4"/>
<w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 4"/>
<w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 4"/>
<w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 4"/>
<w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 4"/>
<w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 4"/>
<w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 4"/>
<w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 4"/>
<w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 4"/>
<w:LsdException Locked="false" Priority="70" Name="Dark List Accent 4"/>
<w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 4"/>
<w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 4"/>
<w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 4"/>
<w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 5"/>
<w:LsdException Locked="false" Priority="61" Name="Light List Accent 5"/>
<w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 5"/>
<w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 5"/>
<w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 5"/>
<w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 5"/>
<w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 5"/>
<w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 5"/>
<w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 5"/>
<w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 5"/>
<w:LsdException Locked="false" Priority="70" Name="Dark List Accent 5"/>
<w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 5"/>
<w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 5"/>
<w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 5"/>
<w:LsdException Locked="false" Priority="60" Name="Light Shading Accent 6"/>
<w:LsdException Locked="false" Priority="61" Name="Light List Accent 6"/>
<w:LsdException Locked="false" Priority="62" Name="Light Grid Accent 6"/>
<w:LsdException Locked="false" Priority="63" Name="Medium Shading 1 Accent 6"/>
<w:LsdException Locked="false" Priority="64" Name="Medium Shading 2 Accent 6"/>
<w:LsdException Locked="false" Priority="65" Name="Medium List 1 Accent 6"/>
<w:LsdException Locked="false" Priority="66" Name="Medium List 2 Accent 6"/>
<w:LsdException Locked="false" Priority="67" Name="Medium Grid 1 Accent 6"/>
<w:LsdException Locked="false" Priority="68" Name="Medium Grid 2 Accent 6"/>
<w:LsdException Locked="false" Priority="69" Name="Medium Grid 3 Accent 6"/>
<w:LsdException Locked="false" Priority="70" Name="Dark List Accent 6"/>
<w:LsdException Locked="false" Priority="71" Name="Colorful Shading Accent 6"/>
<w:LsdException Locked="false" Priority="72" Name="Colorful List Accent 6"/>
<w:LsdException Locked="false" Priority="73" Name="Colorful Grid Accent 6"/>
<w:LsdException Locked="false" Priority="19" QFormat="true"
Name="Subtle Emphasis"/>
<w:LsdException Locked="false" Priority="21" QFormat="true"
Name="Intense Emphasis"/>
<w:LsdException Locked="false" Priority="31" QFormat="true"
Name="Subtle Reference"/>
<w:LsdException Locked="false" Priority="32" QFormat="true"
Name="Intense Reference"/>
<w:LsdException Locked="false" Priority="33" QFormat="true" Name="Book Title"/>
<w:LsdException Locked="false" Priority="37" SemiHidden="true"
UnhideWhenUsed="true" Name="Bibliography"/>
<w:LsdException Locked="false" Priority="39" SemiHidden="true"
UnhideWhenUsed="true" QFormat="true" Name="TOC Heading"/>
<w:LsdException Locked="false" Priority="41" Name="Plain Table 1"/>
<w:LsdException Locked="false" Priority="42" Name="Plain Table 2"/>
<w:LsdException Locked="false" Priority="43" Name="Plain Table 3"/>
<w:LsdException Locked="false" Priority="44" Name="Plain Table 4"/>
<w:LsdException Locked="false" Priority="45" Name="Plain Table 5"/>
<w:LsdException Locked="false" Priority="40" Name="Grid Table Light"/>
<w:LsdException Locked="false" Priority="46" Name="Grid Table 1 Light"/>
<w:LsdException Locked="false" Priority="47" Name="Grid Table 2"/>
<w:LsdException Locked="false" Priority="48" Name="Grid Table 3"/>
<w:LsdException Locked="false" Priority="49" Name="Grid Table 4"/>
<w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark"/>
<w:LsdException Locked="false" Priority="51" Name="Grid Table 6 Colorful"/>
<w:LsdException Locked="false" Priority="52" Name="Grid Table 7 Colorful"/>
<w:LsdException Locked="false" Priority="46"
Name="Grid Table 1 Light Accent 1"/>
<w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 1"/>
<w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 1"/>
<w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 1"/>
<w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 1"/>
<w:LsdException Locked="false" Priority="51"
Name="Grid Table 6 Colorful Accent 1"/>
<w:LsdException Locked="false" Priority="52"
Name="Grid Table 7 Colorful Accent 1"/>
<w:LsdException Locked="false" Priority="46"
Name="Grid Table 1 Light Accent 2"/>
<w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 2"/>
<w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 2"/>
<w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 2"/>
<w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 2"/>
<w:LsdException Locked="false" Priority="51"
Name="Grid Table 6 Colorful Accent 2"/>
<w:LsdException Locked="false" Priority="52"
Name="Grid Table 7 Colorful Accent 2"/>
<w:LsdException Locked="false" Priority="46"
Name="Grid Table 1 Light Accent 3"/>
<w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 3"/>
<w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 3"/>
<w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 3"/>
<w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 3"/>
<w:LsdException Locked="false" Priority="51"
Name="Grid Table 6 Colorful Accent 3"/>
<w:LsdException Locked="false" Priority="52"
Name="Grid Table 7 Colorful Accent 3"/>
<w:LsdException Locked="false" Priority="46"
Name="Grid Table 1 Light Accent 4"/>
<w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 4"/>
<w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 4"/>
<w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 4"/>
<w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 4"/>
<w:LsdException Locked="false" Priority="51"
Name="Grid Table 6 Colorful Accent 4"/>
<w:LsdException Locked="false" Priority="52"
Name="Grid Table 7 Colorful Accent 4"/>
<w:LsdException Locked="false" Priority="46"
Name="Grid Table 1 Light Accent 5"/>
<w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 5"/>
<w:LsdException Locked="false" Priority="48" Name="Grid Table 3 Accent 5"/>
<w:LsdException Locked="false" Priority="49" Name="Grid Table 4 Accent 5"/>
<w:LsdException Locked="false" Priority="50" Name="Grid Table 5 Dark Accent 5"/>
<w:LsdException Locked="false" Priority="51"
Name="Grid Table 6 Colorful Accent 5"/>
<w:LsdException Locked="false" Priority="52"
Name="Grid Table 7 Colorful Accent 5"/>
<w:LsdException Locked="false" Priority="46"
Name="Grid Table 1 Light Accent 6"/>
<w:LsdException Locked="false" Priority="47" Name="Grid Table 2 Accent 6"/>
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<![endif]-->=======================================================================================<br>
<br>
On 03/06/2018 21:31, Nicolas, William (William) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:AD65B49A-3FE8-41DA-9163-90BDEAE82AEB@caltech.edu">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Hey Yehuda,
<div class=""><br class="">
</div>
As Marin is saying this isn’t going to save any space to convert
MRC in TIFF. However, if you happen to want to perform this task,
this is how you can do it:<br class="">
<div class="">
<div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode:
space; line-break: after-white-space;" class="">
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break: after-white-space;"
class="">
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break: after-white-space;"
class="">
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<br class="Apple-interchange-newline">
</div>
</div>
</div>
</div>
</div>
<div class="">Both methods involve ImageJ. You can either use
Bioformat plugin to open .mrc although I don’t like doing that.
Instead there is another plugin called U759_inputoutput.jar (<a
href="http://www.cmib.fr/en/download/softwares/input-output.html"
class="" moz-do-not-send="true">http://www.cmib.fr/en/download/softwares/input-output.html</a>)
that allows you to open .mrc with ImageJ. Then all you got to do
is save as > TIFF.</div>
<div class="">Check if metadata are kept by doing so.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<div dir="auto" style="color: rgb(0, 0, 0); letter-spacing:
normal; text-align: start; text-indent: 0px; text-transform:
none; white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; word-wrap: break-word;
-webkit-nbsp-mode: space; line-break: after-white-space;"
class="">
<div dir="auto" style="color: rgb(0, 0, 0); letter-spacing:
normal; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; word-spacing:
0px; -webkit-text-stroke-width: 0px; word-wrap:
break-word; -webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<div dir="auto" style="color: rgb(0, 0, 0);
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
word-wrap: break-word; -webkit-nbsp-mode: space;
line-break: after-white-space;" class="">
<div dir="auto" style="color: rgb(0, 0, 0);
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; word-wrap: break-word; -webkit-nbsp-mode: space;
line-break: after-white-space;" class="">
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<span style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none;
display: inline !important;" class="">William
Nicolas, HHMI Postdoc.</span></div>
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<span style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none;
display: inline !important;" class=""><br class="">
</span></div>
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<span style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; letter-spacing: normal;
text-align: start; text-indent: 0px;
text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
float: none; display: inline !important;" class=""><b
class=""><u class="">Jensen Laboratory -
Meyerowitz Laboratory</u></b></span></div>
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<span style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none;
display: inline !important;" class="">Division of
Biology and Biological Engineering</span></div>
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<span style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none;
display: inline !important;" class="">1200 East
California Blvd</span></div>
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<span style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none;
display: inline !important;" class="">Postal code:
156-29</span></div>
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<span style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none;
display: inline !important;" class="">California
Institute of Technology</span></div>
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<span style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; float: none;
display: inline !important;" class="">Pasadena, CA
91125, USA</span></div>
<div dir="auto" style="word-wrap: break-word;
-webkit-nbsp-mode: space; line-break:
after-white-space;" class="">
<br style="color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px;" class="">
</div>
</div>
</div>
</div>
<br class="Apple-interchange-newline">
</div>
<br class="Apple-interchange-newline">
<br class="Apple-interchange-newline">
</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">Le 3 juin 2018 à 03:18, Marin van Heel <<a
href="mailto:marin.vanheel@googlemail.com" class=""
moz-do-not-send="true">marin.vanheel@googlemail.com</a>>
a écrit :</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="moz-cite-prefix" style="caret-color: rgb(0, 0,
0); font-family: Helvetica; font-size: 12px; font-style:
normal; font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); text-decoration:
none;">
<br class="">
Dear Yehuda Halfon<br class="">
<br class="">
The em2em converter (<a href="http://image-science.de/"
class="" moz-do-not-send="true">Image-Science.de</a>)
should do the trick but storing (4-bit/8-bit?) MRC
movies in tiff is not a good idea: very few programs can
handle tiff stacks. Moreover if the TIFFs are not
compressed you will not necessarily win any space. You
are probably best off using a standard loss-less
compression program ("zip"), and convert them back when
you need it again. You must always keep your original
raw data "forever" in a loss-less form.<br class="">
<br class="">
Marin van Heel<br class="">
<br class="">
<br class="">
On 03/06/2018 06:02, Yehuda Halfon wrote:<br class="">
</div>
<blockquote type="cite"
cite="mid:01BBF0151AB05848A85DEBB14EE24C42389C01D8@ibwmbx03"
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant-caps: normal;
font-weight: normal; letter-spacing: normal; orphans:
auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; background-color:
rgb(255, 255, 255); text-decoration: none;" class="">
<div style="direction: ltr; font-family: Tahoma;
font-size: 10pt;" class="">Hi there,
<div class=""><br class="">
<div class="">We have a bunch of MRC movie files the
are eating at out storage, and since more are
coming I was wondering if there is a good way to
convert them into tiff to save space?</div>
<div class=""><br class="">
</div>
<div class="">I know that the best way is to save
them directly as tif from EPU/ serialEM and that
is what we will to in the future. But we need to
find a solution to the ones we have now. </div>
<div class=""><br class="">
</div>
<div class="">Thanks, </div>
<div class=""><br class="">
</div>
<div class="">Yehuda Halfon</div>
</div>
</div>
<br class="">
<hr class="">
<p class="" align="center">To unsubscribe from the CCPEM
list, click the following link:<br class="">
<a
href="https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1"
target="_blank" moz-do-not-send="true" class="">https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1</a></p>
</blockquote>
<p style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: normal;
letter-spacing: normal; text-align: start; text-indent:
0px; text-transform: none; white-space: normal;
word-spacing: 0px; -webkit-text-stroke-width: 0px;
background-color: rgb(255, 255, 255); text-decoration:
none;" class="">
<br class="">
</p>
</div>
</blockquote>
</div>
</div>
</blockquote>
--
<pre class="moz-signature" cols="72">==============================================================
Prof Dr Ir Marin van Heel
Laboratório Nacional de Nanotecnologia - LNNano
CNPEM/LNNano, Campinas, Brazil
--------------------------------------------------
Emeritus Professor of Cryo-EM Data Processing
Leiden University
--------------------------------------------------
Emeritus Professor of Structural Biology
Imperial College London
--------------------------------------------------
I receive many emails per day and, although I try,
there is no guarantee that I will actually read each incoming email. </pre>
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