Manual Zeiss Axi Zm.V16 micrscpe and ZEN 2 Pr sftware 15-9-2015 Fred Hartjes EMS 3 Caxial illum. Ring illum. Starting up Pwer n Actuate the knb n the EMS 3 cntrl unit Switch n the caxial illuminatin Switch n the ring illuminatin at the VisiLED MC100 unit Lgin n the PC under yur wn accunt. Lgin under timepix des nt wrk. First switch n the EMS 3 unit befre lgging in. Open ZEN 2 Pr All prgrams => Carl Zeiss Micrscpy => ZEN2 => ZEN (blue editin) In case the selectin windw fr varius versins pps up: select <ZEN 2 pr> Check the crrect sftware versin. In certain cases (like lgging in under timepix) nly ZEN Lite is laded which has limited perfrmance. If requested select <Calibrate Nw> n the ppup windw. Check the Light Path (main tab Lcate) fr any failures In case f a brken camera symbl => rebt the PC If yu use ZEN fr the first time, the camera image will be upside dwn. T crrect check the blue camera tab, press Shw All in the tab header, and press Mdel Specific at the bttm f the menu. At Orientatin change frm riginal t Rtate 180. This nly has t be dne fr the first lgin. Check the path fr string pictures (see Strage Flder: in the dark grey bar at the bttm f the ZEN Windw) Recmmended: Tls => Optins => Saving => Aut Save Path => D:\Zeiss pictures. Otherwise yur Nikhef raming lgin prfile will be sn verladed with pictures. Standard peratin SYCOP 3 unit fr zming and fcussing This is the main cntrl unit f the micrscpe. It is switched n at the EMS 3 bx. Nte that it displays nt nly the magnificatin but als the fcus depth and the reslutin f the image. Fr a practical display the Hme tab is recmmended. Zm: jy stick left/right Carse fcus: jy stick frward/backward Fine fcus: wheel left r right frm the jy stick 1
Nte: yu may als adjust the fcus with the muse wheel while keeping the CTRL key pressed Viewing Camera image and image thrugh eye pieces cannt be viewed simultaneusly. Pull the slide t the right fr camera viewing. The fcus value f the camera is abut 20 µm bigger than the fcus in the eye piece mde. Fr rapid fcussing and image selectin viewing thrugh the lens is recmmended. Nte: the magnificatin (max 180x) refers t the image n the eye pieces, nt t the camera image. Diaphragm. Yu may use the diaphragm (wheel at the right side f the Axi-Zm head) t squeeze the light path, thus increasing the depth f fcus but als deterirating the reslutin. When active the diaphragm symbl appears at the SYCOP 3 display at Reslutin. Nte that when zming ut the diaphragm becmes much mre dminant, reducing the light level f the micrscpe. Illuminatin There are tw illuminatin surces that can bth be tuned in intensity. In mst cases the balance between these tw surces has big effect n the image quality. Take yur time t find the best setting. Thrugh the lens by the unit n the left. Culd be blcked by the slide COAX n the micrscpe head. Ring illuminatin by the VisiLED MC 1000 unit. Culd either a full ring, r any ring sectr t create a shadw. Viewing an image: press the Live buttn Tggle full screen => F11 Camera settings. The camera has very many ptins. Mst imprtant are: Expsure Time Aut expsure is practical t avid change in light level during zming. But it slws dwn the image display. The camera takes an average f the full image fr this, but yu may als select certain area f yur image as a reference. In this case yu have t select the Sptmeter/Fcus ROI buttn and mve the red rectangle t the required psitin. White Balance. Yu may either set this t Aut. Here the three fundamental clurs are autmatically adjusted t equal prprtins. Yu may like this r nt. 5500K. Here the real clurs f the bject are displayed. 2
Creating image files and string them n disk Press Snap => picture will be stred in RAM and appears in the Images and Dcuments tab n right hand f the ZEN windw. Be careful when saving. Default extensin is Zeiss czi which yu cannt pen with anything else but ZEN. S use jpg r png. Adjusting image brightness and cntrast. Yu may further adjust things like cntrast by the dynamic histgram at the bttm f the ZEN windw. Fcussing functins Bth methds (Autfcusing and Manual Extended Fcus) require a surface having certain visible structure like scratches, grains r tiny dust particles. Therefre the fcussing methds d nt wrk n shiny surfaces and flat, transparent bjects. Autfcusing Main tab Lcate. Sub tab: Live Rughly fcus the micrscpe n the desired pint. Set fcussing parameters n the Sftware Autfcus tab Recmmended settings fr accurate Z measurement are shwn n the right picture Click n Autfcus/ROI and select the Sptmeter/Fcus ROI buttn. Subsequently mve the red rectangle t the required psitin. T execute the autfcus prcedure, press n Find Fcus. After cmpletin (see the prgress bar at the bttm f the ZEN windw), the fcus value is read ut as the Z- Psitin n the Sycp 3. Creating an extended fcus image With this methd ne creates an image where items n different height are still all shwn in fcus. T get this, a number f images is acquired at different fcal heights where each new image is used t update a master image. Fr the sftware licence that is built in (Manual Extended Fcus), the images have t be created by manual actin. Main tab: Lcate, set Live n and fcus the micrscpe t abut the Z-centre f the bject Determine yur fcussing strategy: What is the range f fcus f all items yu want t see in the final image? What is a suited step height yu want t apply (e.g. ne r tw clicks f the fine fcus wheel)? Deselect Aut Expsure at the Camera menu and set the light level f yur image t an apprpriate value. 3
Set Live ff and pen the blue tab Manual Extended Depth f Fcus Set Mde: F12 Key Press Start. Tw images will appear: the right ne is the actual image direct frm the camera, the left ne is the resulting master image (befre having any picture acquired this is an lder image). Press the F12 key t acquire a new image. Every time this is dne the master image disappears fr a mment and returns when it is updated with newly acquired image. Change the fcus with the fine fcus wheel and press F12 again t cllect a new image at a different fcus height. Yu will see that the master image gradually imprves when the infrmatin f mre and mre different fcal heights is added t it. Cntinue with this until yu are satisfied with the master image. Terminate the prcess by pressing n Stp. The master image is stred in the Images and Dcuments tab n the right side f the ZEN windw. 4
Measuring n the image and adding inf t it Parameters like the magnitude f a subject, distance between tw items r the diameter f a hle can be easily measured. The measured values take int accunt the actual micrscpe magnificatin. Stre the image using the Snap buttn. This may als be an extended fcus image. G t Graphics n the main menu and select the desired functin. Als items like rectangles, circles, arrws, text, date and ther inf can be added. Select which measurement yu want t display by the right muse buttn => Chse Measurement Features. Yu may frmat the clur and the psitin f the text by the right muse buttn => Frmat Graphical Elements. Nte Select Burn-in Anntatins if yu are satisfied with the image. A new image is created cntaining all added items. The mst recent versin f this manual can be fund at http://www.nikhef.nl/~i56/datasurces/zeiss_dcumentatin/ 5