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--- cryosparc [2021/10/28 10:03] – bonnefon
+++ cryosparc [2024/08/07 15:51] (current) – Luc Bonnefond
@@ Line 1: / Line 1: @@
-Gain/defect files coming from Glacios must be flipped along Y axis when imported in cryoSPARC.
+====== using cryoSPARC ======
+===== modify the particles.star file from Warp =====
+The particles.star files generated by Warp during the on-the-fly processing link each particle to its tif movie. To import the particles in cryoSPARC and keep the link with the motion corrected micrographs, the star file must be edited.
+To edit the particles.star file in **vi** type: <code>vi allparticles_BoxNet2Mask_*.star</code> or <code>vi goodparticles_BoxNet2Mask_*.star</code>
+Change the location of movies to the motion corrected ones:
+<code>
+:
+%s/ <first_characters_of_movie_files>/ average\/<first_characters_of_movie_files>
+</code>
+Change the file type of the motion corrected micrographs:
+<code>
+:
+%s/tif/mrc
+</code>
+Save the changes and close **vi**:
+<code>
+:
+wq!
+</code>
+You can now import the particles in **cryoSPARC** using the **Import Particle Stack** job and parameters:
+  * Micrograph data path: <quote>average/<first_characters_of_movie_files>*.mrc</quote>
+  * Particle meta path: <quote>goodparticles_BoxNet2Mask_*.star</quote>
+  * Particle data path: <quote>particles/</quote>
+  * Check : <quote>Remove leading UID in input micrograph file name</quote>
+----
+===== Reduce the size of a particle stack subset =====
+To reduce the size of the space required on the SSD cache if you are working with a subset of the full extracted particles stack (after selecting a subset of particles with <quote>2D classification</quote> job for example)
+  * Run a <quote>Downsample Particles</quote> job on the subset (output of <quote>select 2D</quote> job in my previous example) without specifying any downsampling.
+The output can be used for further processing and will be smaller and thus faster to load on the scratch. Otherwise the full stask will be loaded in the scratch event thoush only part of it will be used.
+----
+===== Generate a defect file for cryoSPARC =====
+Gain/defect files coming from Glacios must be flipped along Y axis when imported in cryoSPARC.
 Gain file is by default named CountRef...mrc (with a pixel size of 1)
@@ Line 161: / Line 203: @@
 Digital Micrograph(TM), GMS v 3.32
 SUBIMAGE: Subtract section B from section A.            28-Oct-21  11:42:19
 </code>