Update README.md

README.md

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-# swissfel-sfx-tools
+**swissfel-sfx-tools**
 
 A growing collection of tools for processing serial crystallography data at SwissFEL.
 
 At present the toolbox is composed of different folders that very loosely group the scripts into different tasks. These are - as of 01.02.2024:
-- beamline-tools
-- cells
-- clen-tools
-- cool-tools
-- geom-files
-- pyfai-tools
-- reduction-tools
+- beamline-tools => useful for beamline task - not for users
+- cells => common crystfel .cell files used at the beamline
+- clen-tools => tools to calculate the detector distance of a dataset
+- cool-tools => need to update - probably going to be 'analysis tools' in the future
+- geom-files => saved geometry files from past beamtimes
+- pyfai-tools => useful for getting initial beam centre and detector distance use LaB6 powder diffraction and pyFAI
+- reduction-tools => all scripts for getting pattern to integrated reflections
 
+The vast majority are python scripts and use either in Cristallina or Alvra python environment provided at the beamtime.
+A Cristallina environment that should always work can be loaded using:
+
+`source /sf/cristallina/applications/mx/conda/miniconda/bin/activate`
+`conda activate crmx38-analysis`